diff --git a/chemicaltoolbox/opsin/.shed.yml b/chemicaltoolbox/opsin/.shed.yml
new file mode 100644
index 0000000000..18e1f73aa1
--- /dev/null
+++ b/chemicaltoolbox/opsin/.shed.yml
@@ -0,0 +1,16 @@
+categories:
+  - Computational chemistry
+homepage_url: https://github.com/dan2097/opsin
+name: opsin
+owner: bgruening
+remote_repository_url: https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox/opsin
+type: unrestricted
+repositories:
+  opsin:
+    description: OPSIN (Open Parser for Systematic IUPAC Nomenclature) IUPAC name-to-structure conversion
+    long_description: |
+      OPSIN is an Open Parser for Systematic IUPAC Nomenclature.
+      This suite provides tools to convert IUPAC chemical names into machine-readable structures,
+      including SMILES, CML, and InChI formats.
+    include:
+      - opsin.xml
\ No newline at end of file
diff --git a/chemicaltoolbox/opsin/opsin.xml b/chemicaltoolbox/opsin/opsin.xml
index 39f184bbb1..452bf938a2 100644
--- a/chemicaltoolbox/opsin/opsin.xml
+++ b/chemicaltoolbox/opsin/opsin.xml
@@ -1,8 +1,11 @@
-<tool id="ctb_opsin" name="IUPAC name-to-structure" version="2.4.0">
-    <description>converter (OPSIN)</description>
+<tool id="ctb_opsin" name="opsin" version="@TOOL_VERSION@+galaxy0" profile="25.1">
+    <description>IUPAC name-to-structure</description>
+    <macros>
+        <token name="@TOOL_VERSION@">2.9.0</token>
+    </macros>
     <parallelism method="multi" split_inputs="infile" split_mode="to_size" split_size="1000" merge_outputs="outfile"></parallelism>
     <requirements>
-        <requirement type="package" version="2.4.0">opsin</requirement>
+        <requirement type="package" version="@TOOL_VERSION@">opsin</requirement>
     </requirements>
     <stdio>
         <exit_code range="1:" />
@@ -13,15 +16,15 @@
     <command>
 <![CDATA[
         opsin
-            "${radicals}"
-            "${wildcards}"
+            ${radicals}
+            ${wildcards}
             -o$oformat
-            < "${infile}"
-            > "${outfile}"
+           < '${infile}'
+           > '${outfile}'
 ]]>
     </command>  
     <inputs>
-        <param format="tabular,text" name="infile" type="data" label="IUPAC names" help="Upload file with a list of IUPAC names, each on its own line."/>
+        <param format="tabular,txt" name="infile" type="data" label="IUPAC names" help="Upload file with a list of IUPAC names, each on its own line."/>
         <param name="oformat" type="select" label="Output format">
             <option value="smi">SMILES</option>
             <option value="cml">Chemical Markup Language</option>
@@ -53,7 +56,7 @@
 
 OPSIN_ is a IUPAC name-to-structure conversion tool offering high recall and precision on organic chemical nomenclature.
 
-.. _OPSIN: https://bitbucket.org/dan2097/opsin/overview
+.. _OPSIN: https://github.com/dan2097/opsin
 
 
 ]]>
diff --git a/tools/3dtrees_metadata/.shed.yml b/tools/3dtrees_metadata/.shed.yml
new file mode 100644
index 0000000000..b644d6ea25
--- /dev/null
+++ b/tools/3dtrees_metadata/.shed.yml
@@ -0,0 +1,13 @@
+name: 3dtrees_metadata
+owner: bgruening
+description: Extract administrative and ecoregion metadata for 3Dtrees collections.
+homepage_url: https://github.com/3dTrees-earth/3dtrees_metadata
+long_description: |
+  Extracts administrative and ecoregion context for a 3Dtrees collection summary
+  by computing the collection centroid from collection_summary.json and
+  intersecting it with selected GADM and WWF Terrestrial Ecoregions v2.0 vector
+  datasets.
+remote_repository_url: https://github.com/3dTrees-earth/galaxytools/tree/3dtrees_metadata_v1_0_0/tools/3dtrees_metadata
+type: unrestricted
+categories:
+- "Geo Science"
diff --git a/tools/3dtrees_metadata/3dtrees_metadata.xml b/tools/3dtrees_metadata/3dtrees_metadata.xml
new file mode 100644
index 0000000000..4236516eff
--- /dev/null
+++ b/tools/3dtrees_metadata/3dtrees_metadata.xml
@@ -0,0 +1,106 @@
+<tool id="3dtrees_metadata" name="3Dtrees: Metadata" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="24.2">
+    <description>Extract administrative and ecoregion metadata for a point-cloud collection</description>
+    <macros>
+        <token name="@TOOL_VERSION@">1.0.0</token>
+        <token name="@VERSION_SUFFIX@">0</token>
+    </macros>
+    <requirements>
+        <container type="docker">ghcr.io/3dtrees-earth/3dtrees_metadata:@TOOL_VERSION@</container>
+    </requirements>
+    <command detect_errors="exit_code"><![CDATA[
+        ln -s '$collection_summary' collection_summary.json &&
+        python -u /src/run.py
+        --collection-summary collection_summary.json
+        --metadata-layers '$metadata_layers'
+        --output-file additional_metadata.json
+        2>&1
+    ]]></command>
+    <inputs>
+        <param name="collection_summary" type="data" format="json" label="Collection summary" help="collection_summary.json from the 3Dtrees: LAS/LAZ Standardization collection mode."/>
+        <param argument="--metadata-layers" type="select" multiple="true" display="checkboxes" min="1" label="Metadata layers to extract" help="Choose at least one metadata layer. Both are selected by default.">
+            <option value="gadm" selected="true">GADM administrative boundaries</option>
+            <option value="ecoregion" selected="true">WWF Terrestrial Ecoregions v2.0</option>
+        </param>
+    </inputs>
+    <outputs>
+        <data name="additional_metadata" format="json" label="additional_metadata" from_work_dir="additional_metadata.json"/>
+    </outputs>
+    <tests>
+        <test expect_num_outputs="1">
+            <param name="collection_summary" value="collection_summary.json" ftype="json"/>
+            <param name="metadata_layers" value="gadm,ecoregion"/>
+            <output name="additional_metadata" ftype="json">
+                <assert_contents>
+                    <has_text text='"matched": true'/>
+                    <has_text text='"selected_level": 1'/>
+                    <has_text text='"name": "Baden-Wuerttemberg"'/>
+                    <has_text text='"ecoregion_name": "Black Forest"'/>
+                    <has_text text='"biome_name": "Temperate Broadleaf &amp; Mixed Forests"'/>
+                    <has_text text='"is_forest_biome": true'/>
+                </assert_contents>
+            </output>
+        </test>
+        <test expect_num_outputs="1">
+            <param name="collection_summary" value="collection_summary.json" ftype="json"/>
+            <param name="metadata_layers" value="gadm"/>
+            <output name="additional_metadata" ftype="json">
+                <assert_contents>
+                    <has_text text='"admin"'/>
+                    <has_text text='"selected_level": 1'/>
+                    <has_text text='"name": "Baden-Wuerttemberg"'/>
+                    <not_has_text text='"ecoregion"'/>
+                </assert_contents>
+            </output>
+        </test>
+        <test expect_num_outputs="1">
+            <param name="collection_summary" value="collection_summary.json" ftype="json"/>
+            <param name="metadata_layers" value="ecoregion"/>
+            <output name="additional_metadata" ftype="json">
+                <assert_contents>
+                    <has_text text='"ecoregion_name": "Black Forest"'/>
+                    <has_text text='"is_forest_biome": true'/>
+                    <not_has_text text='"admin"'/>
+                </assert_contents>
+            </output>
+        </test>
+    </tests>
+    <help format="markdown"><![CDATA[
+**What it does**
+
+This tool reads a 3Dtrees `collection_summary.json`, computes the WGS84 centroid
+from `collection.multipolygon_wkt`, and intersects that point with the selected
+reference layers. GADM provides administrative context; WWF Terrestrial
+Ecoregions v2.0 data provides ecoregion, realm, and biome context.
+
+-----
+
+**Input**
+
+- **Collection summary**: `collection_summary.json` produced by the 3Dtrees
+  standardization tool in collection mode.
+- **Metadata layers to extract**: one or more internal reference layers. The tool
+  reads the selected reference datasets from the Docker image.
+
+-----
+
+**Output**
+
+The tool writes `additional_metadata.json` with:
+
+- GADM source details and checked layers
+- Collection centroid longitude/latitude in EPSG:4326
+- Whether the centroid matched a GADM feature
+- Selected administrative level and hierarchy
+- Raw matched GADM fields for downstream metadata enrichment
+- Optional WWF ecoregion name/id, realm, biome code/name, and forest-biome flag
+    ]]></help>
+    <creator>
+        <person name="Kilian Gerberding" email="kilian.gerberding@geosense.uni-freiburg.de" url="https://orcid.org/0009-0002-5001-2571"/>
+        <organization name="3Dtrees-Team, University of Freiburg" url="https://github.com/3dTrees-earth"/>
+    </creator>
+    <citations>
+        <citation type="bibtex">
+            @misc{3dtrees_metadata, title = {3Dtrees: Metadata}, author = {3Dtrees Project}, year = {2026}}
+        </citation>
+    </citations>
+</tool>
diff --git a/tools/3dtrees_metadata/test-data/collection_summary.json b/tools/3dtrees_metadata/test-data/collection_summary.json
new file mode 100644
index 0000000000..d3db2a25a9
--- /dev/null
+++ b/tools/3dtrees_metadata/test-data/collection_summary.json
@@ -0,0 +1,8 @@
+{
+  "collection": {
+    "multipolygon_wkt": "MULTIPOLYGON(((7.84 47.98, 7.86 47.98, 7.86 48.00, 7.84 48.00, 7.84 47.98)))"
+  },
+  "n_tiles": 2,
+  "homogeneous_crs": true,
+  "homogeneous_attribute_names": true
+}
diff --git a/tools/3dtrees_metadata/test-data/gadm_fixture.geojson b/tools/3dtrees_metadata/test-data/gadm_fixture.geojson
new file mode 100644
index 0000000000..80656cdc6b
--- /dev/null
+++ b/tools/3dtrees_metadata/test-data/gadm_fixture.geojson
@@ -0,0 +1,35 @@
+{
+  "type": "FeatureCollection",
+  "name": "gadm_fixture",
+  "crs": {
+    "type": "name",
+    "properties": {
+      "name": "urn:ogc:def:crs:OGC:1.3:CRS84"
+    }
+  },
+  "features": [
+    {
+      "type": "Feature",
+      "properties": {
+        "GID_0": "DEU",
+        "COUNTRY": "Germany",
+        "GID_1": "DEU.1_1",
+        "NAME_1": "Baden-Wuerttemberg",
+        "TYPE_1": "Land",
+        "ENGTYPE_1": "State"
+      },
+      "geometry": {
+        "type": "Polygon",
+        "coordinates": [
+          [
+            [7.70, 47.80],
+            [8.00, 47.80],
+            [8.00, 48.20],
+            [7.70, 48.20],
+            [7.70, 47.80]
+          ]
+        ]
+      }
+    }
+  ]
+}
diff --git a/tools/3dtrees_metadata/test-data/wwf_ecoregions_fixture.geojson b/tools/3dtrees_metadata/test-data/wwf_ecoregions_fixture.geojson
new file mode 100644
index 0000000000..0c4b464112
--- /dev/null
+++ b/tools/3dtrees_metadata/test-data/wwf_ecoregions_fixture.geojson
@@ -0,0 +1,34 @@
+{
+  "type": "FeatureCollection",
+  "name": "wwf_ecoregions_fixture",
+  "crs": {
+    "type": "name",
+    "properties": {
+      "name": "urn:ogc:def:crs:OGC:1.3:CRS84"
+    }
+  },
+  "features": [
+    {
+      "type": "Feature",
+      "properties": {
+        "ECO_NAME": "Black Forest",
+        "ECO_ID": "PA0414",
+        "REALM": "PA",
+        "BIOME": 4,
+        "BIOME_DESC": "Temperate Broadleaf & Mixed Forests"
+      },
+      "geometry": {
+        "type": "Polygon",
+        "coordinates": [
+          [
+            [7.70, 47.80],
+            [8.00, 47.80],
+            [8.00, 48.20],
+            [7.70, 48.20],
+            [7.70, 47.80]
+          ]
+        ]
+      }
+    }
+  ]
+}
diff --git a/tools/3dtrees_raycloudtools/raycloudtools.xml b/tools/3dtrees_raycloudtools/raycloudtools.xml
index b5df74a042..4d1ee48ba2 100644
--- a/tools/3dtrees_raycloudtools/raycloudtools.xml
+++ b/tools/3dtrees_raycloudtools/raycloudtools.xml
@@ -1,8 +1,8 @@
 <tool id="3dtrees_raycloudtools" name="3Dtrees: RayCloudTools" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="25.1" license="BSD-3-Clause">
     <description>Tree instance segmentation</description>
     <macros>
-        <token name="@TOOL_VERSION@">1.1.1</token>
-        <token name="@VERSION_SUFFIX@">1</token>
+        <token name="@TOOL_VERSION@">1.2.0</token>
+        <token name="@VERSION_SUFFIX@">0</token>
     </macros>
     <requirements>
         <container type="docker">
diff --git a/tools/3dtrees_raycloudtools/test-data/Example_Tree_RCT_mesh.ply b/tools/3dtrees_raycloudtools/test-data/Example_Tree_RCT_mesh.ply
index 6e1465409e..5c82310e83 100644
Binary files a/tools/3dtrees_raycloudtools/test-data/Example_Tree_RCT_mesh.ply and b/tools/3dtrees_raycloudtools/test-data/Example_Tree_RCT_mesh.ply differ
diff --git a/tools/3dtrees_raycloudtools/test-data/Example_Tree_RCT_segmented.laz b/tools/3dtrees_raycloudtools/test-data/Example_Tree_RCT_segmented.laz
index b11e6010a4..35f73a5d3c 100644
Binary files a/tools/3dtrees_raycloudtools/test-data/Example_Tree_RCT_segmented.laz and b/tools/3dtrees_raycloudtools/test-data/Example_Tree_RCT_segmented.laz differ
diff --git a/tools/3dtrees_raycloudtools/test-data/Example_Tree_RCT_trees.txt b/tools/3dtrees_raycloudtools/test-data/Example_Tree_RCT_trees.txt
index 93abc70313..fc06dc2c8e 100644
--- a/tools/3dtrees_raycloudtools/test-data/Example_Tree_RCT_trees.txt
+++ b/tools/3dtrees_raycloudtools/test-data/Example_Tree_RCT_trees.txt
@@ -1,3 +1,3 @@
 # Tree file. Optional per-tree attributes (e.g. 'height,crown_radius, ') followed by 'x,y,z,radius' and any additional per-segment attributes:
 x,y,z,radius,parent_id,section_id
--0.0004,-0.0005,-0.0400,0.0525,-1,0, 0.0008,-0.0009,0.5044,0.0525,0,1, 0.0300,-0.0450,0.7800,0.0523,1,2, 0.0033,-0.0052,1.0377,0.0523,2,3, -0.0056,0.0493,1.2587,0.0384,3,4, 0.0203,-0.0530,1.2240,0.0356,3,5, -0.0260,0.1583,1.4181,0.0384,4,6, -0.0100,-0.0580,1.4800,0.0356,5,7, -0.0405,0.2458,1.5522,0.0384,6,8, -0.0133,-0.0633,1.7300,0.0356,7,9, -0.0558,0.3339,1.6914,0.0384,8,10, -0.0100,-0.0750,1.8750,0.0355,9,11, -0.0221,0.3834,1.8933,0.0319,10,12, -0.0650,0.4650,1.8400,0.0213,10,14, 0.0175,-0.1334,2.0886,0.0355,11,13, 0.0276,0.3805,2.0381,0.0319,12,15, -0.0950,0.5225,1.9500,0.0213,13,17, 0.0300,-0.1200,2.2040,0.0351,14,16, 0.0157,0.3912,2.1720,0.0319,15,18, -0.1050,0.6050,2.0400,0.0211,16,20, 0.0461,-0.1344,2.3103,0.0351,17,19, -0.0325,0.3050,2.3100,0.0316,18,21, -0.1200,0.6750,2.1250,0.0211,19,23, 0.0367,-0.2200,2.4633,0.0347,20,22, 0.0049,0.2169,2.5093,0.0313,21,24, -0.1633,0.7333,2.1900,0.0184,22,26, -0.1178,0.7124,2.2245,0.0103,22,30, 0.0550,-0.2675,2.5850,0.0267,23,25, 0.0640,-0.2840,2.5760,0.0222,23,28, 0.0450,0.1629,2.5958,0.0225,24,27, -0.0518,0.1240,2.6016,0.0214,24,32, -0.2225,0.8475,2.2725,0.0184,25,31, -0.1100,0.7225,2.3075,0.0103,26,36, 0.0750,-0.3200,2.7600,0.0267,27,29, 0.0520,-0.3640,2.7140,0.0222,28,34, 0.0250,0.2600,2.7400,0.0225,29,33, -0.0750,0.1250,2.7300,0.0214,30,38, -0.2650,0.9375,2.3500,0.0184,31,37, 0.1100,-0.3600,2.8850,0.0267,33,35, -0.0098,-0.4474,2.7674,0.0222,34,40, 0.0600,0.3567,2.8233,0.0225,35,39, -0.1075,0.1300,2.7900,0.0213,36,43, -0.2833,1.0000,2.4233,0.0152,37,42, -0.3100,0.9933,2.4167,0.0102,37,47, 0.1250,-0.4050,3.0050,0.0267,38,41, -0.0400,-0.5100,2.8120,0.0222,39,45, 0.0967,0.4467,2.8733,0.0191,40,44, 0.0497,0.4464,2.9199,0.0119,40,50, -0.1704,0.1585,2.8855,0.0213,41,49, -0.2948,1.0738,2.4693,0.0152,42,48, 0.1340,-0.4420,3.2000,0.0267,44,46, -0.1120,-0.6360,2.9080,0.0222,45,52, 0.0993,0.6170,2.8780,0.0191,46,51, 0.0800,0.4467,2.9733,0.0116,47,56, -0.2000,0.1500,2.9833,0.0201,48,55, -0.3100,1.1300,2.5450,0.0152,49,54, 0.1750,-0.4625,3.3275,0.0243,50,53, -0.1100,-0.7100,2.9833,0.0190,51,58, 0.2000,0.6350,2.9050,0.0180,52,57, 0.0900,0.4800,3.0500,0.0116,53,62, -0.2560,0.1200,3.1040,0.0201,54,61, -0.3287,1.1993,2.5983,0.0152,55,60, 0.1900,-0.4700,3.4467,0.0243,56,59, -0.1280,-0.7820,3.0440,0.0190,57,64, 0.2467,0.7000,2.9333,0.0180,58,63, 0.0833,0.5083,3.1149,0.0116,59,68, -0.2625,0.0650,3.1625,0.0189,60,67, -0.3500,1.2533,2.6300,0.0122,61,66, 0.2580,-0.4800,3.5500,0.0243,62,65, -0.1496,-0.8424,3.1172,0.0190,63,70, 0.3350,0.7950,2.9350,0.0178,64,69, 0.0575,0.5900,3.1525,0.0115,65,74, -0.2450,0.0000,3.2500,0.0182,66,73, -0.3833,1.3667,2.7500,0.0122,67,72, 0.2750,-0.4925,3.6600,0.0188,68,71, 0.3250,-0.4850,3.6100,0.0152,68,77, -0.1967,-0.9933,3.2467,0.0157,69,76, 0.4400,0.7833,2.9000,0.0174,70,75, 0.0900,0.5900,3.2100,0.0115,71,80, -0.2467,-0.0800,3.3333,0.0182,72,79, 0.2800,-0.5250,3.8425,0.0188,74,78, 0.4000,-0.4850,3.6600,0.0152,75,83, -0.2400,-1.0933,3.3033,0.0124,76,82, 0.4900,0.7500,2.8600,0.0174,77,81, -0.2300,-0.1800,3.3950,0.0181,79,85, 0.3033,-0.5533,3.9233,0.0154,80,84, 0.4600,-0.4900,3.7250,0.0120,81,87, 0.5050,0.7000,2.7900,0.0174,83,86, -0.2000,-0.2533,3.4767,0.0181,84,89, 0.3400,-0.5750,4.0200,0.0154,85,88, 0.4750,0.6700,2.7000,0.0169,87,90, -0.1250,-0.4350,3.5750,0.0181,88,92, 0.3550,-0.5975,4.1150,0.0119,89,91, 0.4000,0.6200,2.5833,0.0168,90,93, -0.1033,-0.6267,3.6833,0.0181,91,94, 0.3333,0.5367,2.5033,0.0168,93,95, 0.2625,0.4375,2.4475,0.0168,95,96
+-0.0001,0.0000,0.0170,0.0496,-1,0, -0.0041,0.0072,0.3102,0.0495,0,1, -0.0197,-0.0208,0.5441,0.0495,1,2, 0.0289,-0.0430,0.7817,0.0494,2,3, 0.0022,-0.0065,1.0393,0.0494,3,4, 0.0051,0.0015,1.2568,0.0488,4,5, -0.0355,0.1312,1.3994,0.0358,5,6, -0.0101,-0.0525,1.5017,0.0332,5,7, -0.0500,0.2320,1.5410,0.0358,6,8, 0.0079,-0.0672,1.7355,0.0332,7,9, -0.0558,0.3157,1.6645,0.0358,8,10, -0.0094,-0.0712,1.8755,0.0332,9,11, -0.0546,0.4041,1.8211,0.0358,10,12, 0.0004,-0.1285,2.0667,0.0332,11,13, -0.0065,0.3776,1.9416,0.0299,12,14, -0.1022,0.5328,1.9717,0.0198,12,16, 0.0378,-0.1209,2.2022,0.0328,13,15, 0.0325,0.3806,2.0534,0.0299,14,17, -0.1429,0.5818,2.0170,0.0172,15,19, -0.1034,0.6093,2.0410,0.0099,15,22, 0.0205,-0.1726,2.3263,0.0325,16,18, 0.0152,0.3933,2.1812,0.0299,17,20, -0.1619,0.6444,2.0747,0.0172,18,23, -0.1169,0.6763,2.1220,0.0099,19,26, 0.0358,-0.2209,2.4633,0.0325,20,21, -0.0339,0.3043,2.3098,0.0295,21,24, -0.1719,0.7324,2.1603,0.0172,22,27, -0.1309,0.7083,2.1800,0.0099,23,30, 0.0378,-0.2939,2.5967,0.0324,24,25, 0.0050,0.2054,2.5183,0.0291,25,28, -0.2061,0.8030,2.2447,0.0172,26,31, -0.1394,0.7148,2.2265,0.0099,27,35, 0.0741,-0.3192,2.7585,0.0254,28,29, 0.0044,-0.4309,2.7325,0.0201,28,33, -0.0959,0.2711,2.6203,0.0212,29,32, -0.0667,0.1102,2.6278,0.0197,29,37, -0.2412,0.8838,2.2890,0.0172,30,36, -0.1087,0.7176,2.3004,0.0099,31,41, 0.1111,-0.3567,2.8820,0.0254,32,34, -0.0505,-0.5006,2.8197,0.0201,33,39, -0.0599,0.3073,2.6800,0.0212,34,38, -0.0759,0.1275,2.7308,0.0197,35,43, -0.2785,0.9464,2.3633,0.0172,36,42, 0.1311,-0.3979,3.0303,0.0254,38,40, -0.1134,-0.6227,2.8993,0.0201,39,45, 0.0088,0.3358,2.7843,0.0212,40,44, -0.1168,0.1469,2.7978,0.0197,41,48, -0.2986,1.0128,2.4297,0.0172,42,47, 0.1325,-0.4416,3.1988,0.0254,43,46, -0.1804,-0.6907,2.9590,0.0154,44,50, -0.1290,-0.7122,2.9810,0.0129,44,55, 0.0673,0.3832,2.8496,0.0212,45,49, -0.1692,0.1603,2.8724,0.0197,46,53, -0.3189,1.0668,2.4665,0.0143,47,52, 0.1746,-0.4620,3.3255,0.0231,48,51, -0.2332,-0.7333,3.0066,0.0154,49,56, -0.1234,-0.7687,3.0250,0.0129,50,62, 0.1111,0.4793,2.8910,0.0183,51,54, 0.0530,0.4640,2.9487,0.0108,51,60, -0.2119,0.1345,2.9852,0.0186,52,59, -0.3155,1.1296,2.5242,0.0143,53,58, 0.1881,-0.4689,3.4450,0.0231,54,57, -0.2685,-0.7976,3.0643,0.0132,55,63, -0.1319,-0.8022,3.0560,0.0128,56,69, 0.1035,0.6132,2.8785,0.0182,57,61, 0.0657,0.4271,3.0245,0.0108,58,67, -0.2557,0.1186,3.1072,0.0186,59,66, -0.3249,1.1838,2.5547,0.0116,60,65, 0.2561,-0.4790,3.5498,0.0231,61,64, -0.3055,-0.8886,3.1673,0.0119,62,70, -0.1599,-0.8372,3.0907,0.0128,63,77, 0.2021,0.6373,2.9090,0.0163,64,68, 0.1203,0.7096,2.9366,0.0081,64,75, 0.0876,0.4823,3.0470,0.0107,65,74, -0.2626,0.0635,3.1622,0.0174,66,73, -0.3464,1.2313,2.6100,0.0116,67,72, 0.2761,-0.4969,3.6687,0.0180,68,71, 0.3355,-0.4779,3.6277,0.0146,68,79, -0.3194,-0.9527,3.2475,0.0119,69,78, -0.1739,-0.8872,3.1695,0.0128,70,85, 0.2475,0.7008,2.9343,0.0163,71,76, 0.0959,0.4990,3.1015,0.0107,73,83, -0.2474,-0.0002,3.2480,0.0169,74,82, -0.3529,1.2758,2.6475,0.0116,75,81, 0.2811,-0.5260,3.8443,0.0180,76,80, 0.3971,-0.4827,3.6600,0.0145,77,87, -0.3149,-1.0117,3.2870,0.0119,78,86, 0.3316,0.7948,2.9320,0.0163,80,84, 0.0774,0.5173,3.1315,0.0107,81,91, -0.2519,-0.0817,3.3635,0.0169,82,90, -0.3809,1.3678,2.7503,0.0116,83,89, 0.3048,-0.5389,3.9220,0.0149,84,88, 0.4611,-0.4892,3.7255,0.0115,85,94, -0.2909,-1.0927,3.3260,0.0114,86,93, 0.4388,0.7848,2.8960,0.0161,87,92, 0.0574,0.5888,3.1540,0.0107,88,97, -0.2201,-0.2160,3.4470,0.0169,89,96, 0.3425,-0.5872,4.0420,0.0149,91,95, 0.5006,0.7518,2.8560,0.0161,94,98, 0.0866,0.5908,3.2080,0.0107,95,101, -0.1582,-0.3719,3.5537,0.0169,96,100, 0.3536,-0.5975,4.1153,0.0115,97,99, 0.5081,0.6998,2.7905,0.0161,98,102, -0.0839,-0.6092,3.6685,0.0169,100,103, 0.4781,0.6723,2.7020,0.0156,102,104, 0.4025,0.6241,2.5833,0.0156,104,105, 0.3626,0.5748,2.5310,0.0156,105,106, 0.3116,0.5063,2.4790,0.0156,106,107, 0.2598,0.4308,2.4513,0.0155,107,108
diff --git a/tools/3dtrees_raycloudtools/test-data/Example_Tree_RCT_trees_info.txt b/tools/3dtrees_raycloudtools/test-data/Example_Tree_RCT_trees_info.txt
index 7a41ef5840..7a8a578ed5 100644
--- a/tools/3dtrees_raycloudtools/test-data/Example_Tree_RCT_trees_info.txt
+++ b/tools/3dtrees_raycloudtools/test-data/Example_Tree_RCT_trees_info.txt
@@ -1,3 +1,3 @@
 # Tree file. Optional per-tree attributes (e.g. 'height,crown_radius, ') followed by 'x,y,z,radius' and any additional per-segment attributes:
 height,crown_radius,dimension,monocotal,DBH,bend,branch_slope, x,y,z,radius,parent_id,section_id,volume,diameter,length,strength,min_strength,dominance,angle,children
-5.1550,1.8371,1.7128,0.2588,0.0768,0.0635,1.2881, -0.0004,-0.0005,-0.0400,0.0525,-1,0.0000,0.0320,0.1050,5.5269,0.0334,0.0334,0.2470,41.4593,1.0000, 0.0008,-0.0009,0.5044,0.0525,0,1.0000,0.0047,0.1050,5.5269,0.0334,0.0334,0.0000,0.0000,1.0000, 0.0300,-0.0450,0.7800,0.0523,1,2.0000,0.0024,0.1046,4.9825,0.0369,0.0334,0.0000,0.0000,1.0000, 0.0033,-0.0052,1.0377,0.0523,2,3.0000,0.0023,0.1046,4.7018,0.0391,0.0334,0.0756,35.2632,2.0000, -0.0056,0.0493,1.2587,0.0384,3,4.0000,0.0011,0.0768,4.4397,0.0329,0.0329,0.0000,0.0000,1.0000, 0.0203,-0.0530,1.2240,0.0356,3,5.0000,0.0008,0.0712,4.2204,0.0327,0.0327,0.0000,0.0000,1.0000, -0.0260,0.1583,1.4181,0.0384,4,6.0000,0.0009,0.0768,4.2119,0.0346,0.0329,0.0000,0.0000,1.0000, -0.0100,-0.0580,1.4800,0.0356,5,7.0000,0.0010,0.0712,4.0273,0.0342,0.0327,0.0000,0.0000,1.0000, -0.0405,0.2458,1.5522,0.0384,6,8.0000,0.0007,0.0768,4.0177,0.0363,0.0329,0.0000,0.0000,1.0000, -0.0133,-0.0633,1.7300,0.0356,7,9.0000,0.0010,0.0712,3.7694,0.0366,0.0327,0.0000,0.0000,1.0000, -0.0558,0.3339,1.6914,0.0384,8,10.0000,0.0008,0.0768,3.8570,0.0378,0.0329,0.3833,43.1275,2.0000, -0.0100,-0.0750,1.8750,0.0355,9,11.0000,0.0006,0.0710,3.5194,0.0391,0.0327,0.0000,0.0000,1.0000, -0.0221,0.3834,1.8933,0.0319,10,12.0000,0.0007,0.0638,3.6915,0.0344,0.0329,0.0000,0.0000,1.0000, -0.0650,0.4650,1.8400,0.0213,10,14.0000,0.0003,0.0426,2.5414,0.0369,0.0329,0.0000,0.0000,1.0000, 0.0175,-0.1334,2.0886,0.0355,11,13.0000,0.0009,0.0710,3.3739,0.0408,0.0327,0.0000,0.0000,1.0000, 0.0276,0.3805,2.0381,0.0319,12,15.0000,0.0005,0.0638,3.4809,0.0365,0.0329,0.0000,0.0000,1.0000, -0.0950,0.5225,1.9500,0.0213,13,17.0000,0.0002,0.0426,2.3430,0.0400,0.0329,0.0000,0.0000,1.0000, 0.0300,-0.1200,2.2040,0.0351,14,16.0000,0.0005,0.0702,3.1507,0.0433,0.0327,0.0000,0.0000,1.0000, 0.0157,0.3912,2.1720,0.0319,15,18.0000,0.0004,0.0638,3.3278,0.0381,0.0329,0.0000,0.0000,1.0000, 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0.0450,0.1629,2.5958,0.0225,24,27.0000,0.0002,0.0450,2.8022,0.0349,0.0329,0.0000,0.0000,1.0000, -0.0518,0.1240,2.6016,0.0214,24,32.0000,0.0002,0.0428,2.6783,0.0351,0.0329,0.0000,0.0000,1.0000, -0.2225,0.8475,2.2725,0.0184,25,31.0000,0.0002,0.0368,1.8842,0.0446,0.0329,0.0000,0.0000,1.0000, -0.1100,0.7225,2.3075,0.0103,26,36.0000,0.0000,0.0206,1.0840,0.0502,0.0329,0.0000,0.0000,0.0000, 0.0750,-0.3200,2.7600,0.0267,27,29.0000,0.0004,0.0534,2.6179,0.0424,0.0327,0.0000,0.0000,1.0000, 0.0520,-0.3640,2.7140,0.0222,28,34.0000,0.0002,0.0444,2.1592,0.0448,0.0327,0.0000,0.0000,1.0000, 0.0250,0.2600,2.7400,0.0225,29,33.0000,0.0003,0.0450,2.6926,0.0363,0.0329,0.0000,0.0000,1.0000, -0.0750,0.1250,2.7300,0.0214,30,38.0000,0.0002,0.0428,2.5356,0.0371,0.0329,0.0000,0.0000,1.0000, -0.2650,0.9375,2.3500,0.0184,31,37.0000,0.0001,0.0368,1.7314,0.0485,0.0329,0.3790,26.2442,2.0000, 0.1100,-0.3600,2.8850,0.0267,33,35.0000,0.0003,0.0534,2.4341,0.0456,0.0327,0.0000,0.0000,1.0000, 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-0.1804,-0.6907,2.9590,0.0154,44,50.0000,0.0001,0.0308,1.6989,0.0433,0.0317,0.0000,0.0000,1.0000, -0.1290,-0.7122,2.9810,0.0129,44,55.0000,0.0001,0.0258,1.3915,0.0463,0.0317,0.0000,0.0000,1.0000, 0.0673,0.3832,2.8496,0.0212,45,49.0000,0.0001,0.0424,2.4642,0.0379,0.0317,0.4791,121.4107,2.0000, -0.1692,0.1603,2.8724,0.0197,46,53.0000,0.0001,0.0394,2.3076,0.0383,0.0317,0.0000,0.0000,1.0000, -0.3189,1.0668,2.4665,0.0143,47,52.0000,0.0000,0.0286,1.4920,0.0466,0.0317,0.0000,0.0000,1.0000, 0.1746,-0.4620,3.3255,0.0231,48,51.0000,0.0002,0.0462,1.9726,0.0505,0.0317,0.0000,0.0000,1.0000, -0.2332,-0.7333,3.0066,0.0154,49,56.0000,0.0001,0.0308,1.5863,0.0463,0.0317,0.0000,0.0000,1.0000, -0.1234,-0.7687,3.0250,0.0129,50,62.0000,0.0000,0.0258,1.2693,0.0507,0.0317,0.0000,0.0000,1.0000, 0.1111,0.4793,2.8910,0.0183,51,54.0000,0.0001,0.0366,2.3645,0.0354,0.0317,0.0000,0.0000,1.0000, 0.0530,0.4640,2.9487,0.0108,51,60.0000,0.0000,0.0216,1.5137,0.0372,0.0317,0.0000,0.0000,1.0000, -0.2119,0.1345,2.9852,0.0186,52,59.0000,0.0001,0.0372,2.2154,0.0382,0.0317,0.0000,0.0000,1.0000, -0.3155,1.1296,2.5242,0.0143,53,58.0000,0.0001,0.0286,1.4236,0.0489,0.0317,0.0000,0.0000,1.0000, 0.1881,-0.4689,3.4450,0.0231,54,57.0000,0.0002,0.0462,1.8376,0.0542,0.0317,0.0000,0.0000,1.0000, -0.2685,-0.7976,3.0643,0.0132,55,63.0000,0.0001,0.0264,1.5035,0.0436,0.0317,0.0000,0.0000,1.0000, -0.1319,-0.8022,3.0560,0.0128,56,69.0000,0.0000,0.0256,1.1975,0.0534,0.0317,0.0000,0.0000,1.0000, 0.1035,0.6132,2.8785,0.0182,57,61.0000,0.0001,0.0364,2.2511,0.0370,0.0317,0.6039,26.5431,2.0000, 0.0657,0.4271,3.0245,0.0108,58,67.0000,0.0000,0.0216,1.3851,0.0407,0.0317,0.0000,0.0000,1.0000, -0.2557,0.1186,3.1072,0.0186,59,66.0000,0.0001,0.0372,2.0921,0.0405,0.0317,0.0000,0.0000,1.0000, -0.3249,1.1838,2.5547,0.0116,60,65.0000,0.0000,0.0232,1.3382,0.0444,0.0317,0.0000,0.0000,1.0000, 0.2561,-0.4790,3.5498,0.0231,61,64.0000,0.0002,0.0462,1.7171,0.0580,0.0317,0.2129,60.4668,2.0000, -0.3055,-0.8886,3.1673,0.0119,62,70.0000,0.0001,0.0238,1.4101,0.0430,0.0317,0.0000,0.0000,1.0000, -0.1599,-0.8372,3.0907,0.0128,63,77.0000,0.0000,0.0256,1.1511,0.0556,0.0317,0.0000,0.0000,1.0000, 0.2021,0.6373,2.9090,0.0163,64,68.0000,0.0001,0.0326,2.1164,0.0363,0.0317,0.0000,0.0000,1.0000, 0.1203,0.7096,2.9366,0.0081,64,75.0000,0.0000,0.0162,1.1138,0.0408,0.0317,0.0000,0.0000,0.0000, 0.0876,0.4823,3.0470,0.0107,65,74.0000,0.0000,0.0214,1.2998,0.0430,0.0317,0.0000,0.0000,1.0000, -0.2626,0.0635,3.1622,0.0174,66,73.0000,0.0001,0.0348,1.9615,0.0411,0.0317,0.0000,0.0000,1.0000, -0.3464,1.2313,2.6100,0.0116,67,72.0000,0.0000,0.0232,1.2753,0.0466,0.0317,0.0000,0.0000,1.0000, 0.2761,-0.4969,3.6687,0.0180,68,71.0000,0.0001,0.0360,1.5918,0.0519,0.0317,0.0000,0.0000,1.0000, 0.3355,-0.4779,3.6277,0.0146,68,79.0000,0.0001,0.0292,1.2728,0.0555,0.0317,0.0000,0.0000,1.0000, -0.3194,-0.9527,3.2475,0.0119,69,78.0000,0.0000,0.0238,1.2678,0.0478,0.0317,0.0000,0.0000,1.0000, -0.1739,-0.8872,3.1695,0.0128,70,85.0000,0.0000,0.0256,1.0944,0.0585,0.0317,0.0000,0.0000,0.0000, 0.2475,0.7008,2.9343,0.0163,71,76.0000,0.0001,0.0326,2.0104,0.0382,0.0317,0.0000,0.0000,1.0000, 0.0959,0.4990,3.1015,0.0107,73,83.0000,0.0000,0.0214,1.2363,0.0453,0.0317,0.0000,0.0000,1.0000, -0.2474,-0.0002,3.2480,0.0169,74,82.0000,0.0001,0.0338,1.8834,0.0419,0.0317,0.0000,0.0000,1.0000, -0.3529,1.2758,2.6475,0.0116,75,81.0000,0.0000,0.0232,1.1993,0.0496,0.0317,0.0000,0.0000,1.0000, 0.2811,-0.5260,3.8443,0.0180,76,80.0000,0.0002,0.0360,1.4699,0.0562,0.0317,0.0000,0.0000,1.0000, 0.3971,-0.4827,3.6600,0.0145,77,87.0000,0.0000,0.0290,1.1615,0.0605,0.0317,0.0000,0.0000,1.0000, -0.3149,-1.0117,3.2870,0.0119,78,86.0000,0.0000,0.0238,1.1642,0.0520,0.0317,0.0000,0.0000,1.0000, 0.3316,0.7948,2.9320,0.0163,80,84.0000,0.0001,0.0326,1.9283,0.0398,0.0317,0.0000,0.0000,1.0000, 0.0774,0.5173,3.1315,0.0107,81,91.0000,0.0000,0.0214,1.1787,0.0475,0.0317,0.0000,0.0000,1.0000, -0.2519,-0.0817,3.3635,0.0169,82,90.0000,0.0001,0.0338,1.7754,0.0444,0.0317,0.0000,0.0000,1.0000, -0.3809,1.3678,2.7503,0.0116,83,89.0000,0.0001,0.0232,1.1408,0.0521,0.0317,0.0000,0.0000,0.0000, 0.3048,-0.5389,3.9220,0.0149,84,88.0000,0.0001,0.0298,1.2918,0.0555,0.0317,0.0000,0.0000,1.0000, 0.4611,-0.4892,3.7255,0.0115,85,94.0000,0.0000,0.0230,1.0918,0.0541,0.0317,0.0000,0.0000,0.0000, -0.2909,-1.0927,3.3260,0.0114,86,93.0000,0.0000,0.0228,1.0930,0.0537,0.0317,0.0000,0.0000,0.0000, 0.4388,0.7848,2.8960,0.0161,87,92.0000,0.0001,0.0322,1.8022,0.0422,0.0317,0.0000,0.0000,1.0000, 0.0574,0.5888,3.1540,0.0107,88,97.0000,0.0000,0.0214,1.1390,0.0491,0.0317,0.0000,0.0000,1.0000, -0.2201,-0.2160,3.4470,0.0169,89,96.0000,0.0001,0.0338,1.6340,0.0482,0.0317,0.0000,0.0000,1.0000, 0.3425,-0.5872,4.0420,0.0149,91,95.0000,0.0001,0.0298,1.2096,0.0593,0.0317,0.0000,0.0000,1.0000, 0.5006,0.7518,2.8560,0.0161,94,98.0000,0.0001,0.0322,1.6887,0.0450,0.0317,0.0000,0.0000,1.0000, 0.0866,0.5908,3.2080,0.0107,95,101.0000,0.0000,0.0214,1.0614,0.0527,0.0317,0.0000,0.0000,0.0000, -0.1582,-0.3719,3.5537,0.0169,96,100.0000,0.0002,0.0338,1.4727,0.0535,0.0317,0.0000,0.0000,1.0000, 0.3536,-0.5975,4.1153,0.0115,97,99.0000,0.0000,0.0230,1.0748,0.0549,0.0317,0.0000,0.0000,0.0000, 0.5081,0.6998,2.7905,0.0161,98,102.0000,0.0001,0.0322,1.6080,0.0473,0.0317,0.0000,0.0000,1.0000, -0.0839,-0.6092,3.6685,0.0169,100,103.0000,0.0002,0.0338,1.2739,0.0619,0.0317,0.0000,0.0000,0.0000, 0.4781,0.6723,2.7020,0.0156,102,104.0000,0.0001,0.0312,1.5240,0.0487,0.0317,0.0000,0.0000,1.0000, 0.4025,0.6241,2.5833,0.0156,104,105.0000,0.0001,0.0312,1.4266,0.0520,0.0317,0.0000,0.0000,1.0000, 0.3626,0.5748,2.5310,0.0156,105,106.0000,0.0001,0.0312,1.2779,0.0581,0.0317,0.0000,0.0000,1.0000, 0.3116,0.5063,2.4790,0.0156,106,107.0000,0.0001,0.0312,1.1956,0.0621,0.0317,0.0000,0.0000,1.0000, 0.2598,0.4308,2.4513,0.0155,107,108.0000,0.0001,0.0310,1.0957,0.0674,0.0317,0.0000,0.0000,0.0000
diff --git a/tools/3dtrees_raycloudtools/test-data/Example_Tree_RCT_trees_mesh.ply b/tools/3dtrees_raycloudtools/test-data/Example_Tree_RCT_trees_mesh.ply
index f1ac898d6e..fda4cd9908 100644
Binary files a/tools/3dtrees_raycloudtools/test-data/Example_Tree_RCT_trees_mesh.ply and b/tools/3dtrees_raycloudtools/test-data/Example_Tree_RCT_trees_mesh.ply differ
diff --git a/tools/cellpose_v4/.shed.yml b/tools/cellpose_v4/.shed.yml
index 6155d660fc..785113ced1 100644
--- a/tools/cellpose_v4/.shed.yml
+++ b/tools/cellpose_v4/.shed.yml
@@ -2,13 +2,12 @@ name: cellposesam
 owner: bgruening
 categories:
   - Imaging
-description: CellPose SAM
-remote_repository_url: https://github.com/bgruening/galaxytools/tree/master/tools
+description: Cellpose-SAM
+remote_repository_url: https://github.com/bgruening/galaxytools/tree/master/tools/cellpose_v4
 type: unrestricted
 homepage_url: https://cellpose.org
 long_description: |
     Cellpose-SAM: cell and nucleus segmentation with superhuman generalization. It can be optimized for your own data, applied in 3D, works on images with shot noise, (an)isotropic blur, undersampling, contrast inversions, regardless of channel order and object sizes.
 auto_tool_repositories:
   name_template: "{{ tool_id }}"
-  description_template: "Wrapper for CellPoseSAM {{ tool_name }}."
-
+  description_template: "Wrapper for Cellpose-SAM {{ tool_name }}."
diff --git a/tools/cellpose_v4/cellpose.xml b/tools/cellpose_v4/cellpose.xml
index 486f90e91c..e0dc341eea 100644
--- a/tools/cellpose_v4/cellpose.xml
+++ b/tools/cellpose_v4/cellpose.xml
@@ -2,7 +2,7 @@
     <description>with Cellpose-SAM</description>
     <macros>
         <token name="@TOOL_VERSION@">4.0.8</token>
-        <token name="@VERSION_SUFFIX@">0</token>
+        <token name="@VERSION_SUFFIX@">1</token>
     </macros>
     <requirements>
         <requirement type="package" version="@TOOL_VERSION@">cellpose</requirement> 
@@ -97,7 +97,7 @@
         <param name="diameter" type="float" optional="true" label="Cell or nuclei diameter in pixels" help="Use to resize cells to the training diameter. Leave blank for automated estimation."/>
 	    <param name="no_resample" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Disables flows/cellprob resampling to original image size before computing masks."
 		    help="Using this flag will make more masks more jagged with larger diameter settings."/>
-        <param name="no_interp" type="boolean" truevalue="true" falsevalue="false" checked="true" label="Interpolate when running dynamics."/>
+        <param name="no_interp" type="boolean" truevalue="true" falsevalue="false" checked="false" label="Do not interpolate when running dynamics."/>
         <param name="flow_threshold" type="float" min="0" value="0.4" label="Flow error threshold (all cells with errors below threshold are kept) (not used for 3D)"/>
         <param name="cellprob_threshold" type="float" value="0.0" label="Cell probability threshold (all pixels with prob above threshold kept for masks)"/>
         <param name="niter" type="integer" min="0" value="0" label="Number of iterations"
@@ -137,6 +137,9 @@
 	        <param name="save_tif" value="true"/>
             <output name="cp_tiff" file="image_cp_masks.tiff" compare="image_diff" metric="iou"/>
 	        <output name="cp_png" file="image_cp_masks.png" compare="image_diff" metric="iou"/>
+	        <section name="options">
+		        <param name="no_interp" value="true"/>
+	        </section>
 	    </test>
         <test expect_num_outputs="1">
 	        <param name="img_in" value="image3d.tiff"/>
@@ -159,6 +162,9 @@
 	        <param name="save_outlines" value="true" />
 	        <param name="use_gpu" value="true" />
 	        <param name="detailed_output" value="true" />
+	        <section name="options">
+		        <param name="no_interp" value="true"/>
+	        </section>
 	        <output name="cp_png" file="image_cp_masks.png" compare="image_diff" metric="iou"/>
             <output name="cp_flows" file="image_flows_cp_masks.tiff" compare="image_diff" />
 	        <output name="cp_flows_dp" file="image_dP_cp_masks.tiff" compare="image_diff" />
@@ -177,6 +183,7 @@
             <section name="options">
                 <param name="no_norm" value="false" />
                 <param name="no_resample" value="false" />
+		        <param name="no_interp" value="true"/>
                 <param name="diameter" value="10" />
                 <param name="flow_threshold" value="0.5" />
                 <param name="cellprob_threshold" value="0.0" />
diff --git a/tools/llm_hub/macros.xml b/tools/llm_hub/macros.xml
index 8e26221bea..23b484328c 100644
--- a/tools/llm_hub/macros.xml
+++ b/tools/llm_hub/macros.xml
@@ -1,3 +1,3 @@
 <macros>
-    <token name="@TOOL_VERSION@">2.32.0</token>
+    <token name="@TOOL_VERSION@">2.36.0</token>
 </macros>
diff --git a/tools/logan_proteins/.shed.yml b/tools/logan_proteins/.shed.yml
index f6e1e85566..8feec5dcda 100644
--- a/tools/logan_proteins/.shed.yml
+++ b/tools/logan_proteins/.shed.yml
@@ -13,7 +13,7 @@ long_description: |
     are validated and aligned with MMseqs2.  The approach scales sub-linearly
     with the number of queries, making it practical for large-scale metagenomic
     and comparative-proteomics workflows.
-remote_repository_url: https://github.com/bgruening/galaxytools/tree/master/tools/search_proteins
+remote_repository_url: https://github.com/bgruening/galaxytools/tree/master/tools/logan_proteins
 type: unrestricted
 auto_tool_repositories:
   name_template: "{{ tool_id }}"
diff --git a/tools/logan_proteins/embed_query.xml b/tools/logan_proteins/embed_query.xml
index 4954a1ac87..81e666eae0 100644
--- a/tools/logan_proteins/embed_query.xml
+++ b/tools/logan_proteins/embed_query.xml
@@ -9,10 +9,11 @@
             FORCE_CPU="--force_cpu"
         else
             FORCE_CPU="";
-        fi &&        
+        fi &&
+        ln -s '$query_sequences' query_sequences.fasta &&    
         mkdir -p results &&
         python /app/embed_query.py
-            --query_sequences '$query_sequences'
+            --query_sequences query_sequences.fasta
             --output results
             -F
             \$FORCE_CPU
@@ -50,9 +51,6 @@ This is the first step in a two-step protein search pipeline:
 
 - **Query sequences**: A FASTA file containing protein sequences to be embedded
 
-**Parameters**
-
-- **Force CPU usage**: By default, CPU will be used. Disable this option to use GPU instead if available.
 
 **Outputs**
 
diff --git a/tools/logan_proteins/macros.xml b/tools/logan_proteins/macros.xml
index 813e50fe8e..d791d85d73 100644
--- a/tools/logan_proteins/macros.xml
+++ b/tools/logan_proteins/macros.xml
@@ -1,10 +1,10 @@
 <macros>
-    <token name="@TOOL_VERSION@">1.2.0</token>
+    <token name="@TOOL_VERSION@">1.2.2</token>
     <token name="@VERSION_SUFFIX@">0</token>
     <token name="@PROFILE@">25.0</token>
     <xml name="requirements">
         <requirements>
-            <container type="docker">quay.io/bgruening/logan-protein:1.2.0</container>
+            <container type="docker">quay.io/bgruening/logan-protein:1.2.2</container>
         </requirements>
     </xml>
     <xml name="citations">
diff --git a/tools/logan_proteins/search_database.xml b/tools/logan_proteins/search_database.xml
index b6e1057c05..6da9dc36b0 100644
--- a/tools/logan_proteins/search_database.xml
+++ b/tools/logan_proteins/search_database.xml
@@ -9,11 +9,14 @@
         mkdir -p results/intermediate_files &&       
         ln -s '$query_embeddings_npy' results/intermediate_files/query_embeddings.npy &&
         ln -s '$query_embeddings_names' results/intermediate_files/query_embeddings.names.txt &&
+        ln -s '$query_sequences' query_sequences.fasta &&
         python /app/search_database.py
             --database '$database.fields.path'
+            $deep_search
             --output results/
-            --query_sequences '$query_sequences'
+            --query_sequences query_sequences.fasta
             --num_threads \${GALAXY_SLOTS:-8}
+            --memory \${GALAXY_MEMORY_MB:-16000}
             #if $outfmt:
                 --outfmt '$outfmt'
             #end if
@@ -36,6 +39,7 @@
             <option value="4">SAM (4)</option>
             <option value="5">Taxonomic classification (5)</option>
         </param>
+        <param argument="--deep-search" type="boolean" truevalue="--deep-search" falsevalue="" label="Deep search mode" help="If enabled, extract proteins from all search results instead of only aligned centroids, then align everything with MMseqs2)"/> 
     </inputs>
     
     <outputs>
@@ -49,6 +53,7 @@
             <param name="query_sequences" value="queries.fasta"/>
             <param name="query_embeddings_npy" value="query_embeddings.npy"/>
             <param name="query_embeddings_names" value="query_embeddings.names.txt"/>
+            <param name="deep_search" value="false"/>
             <param name="database" value="faiss-demo-db-20260203"/>
             <param name="outfmt" value="0"/>
             <assert_stdout>
@@ -74,6 +79,7 @@ with MMseqs2. It is the second step in the protein search pipeline.
 - **Original query sequences**: The same FASTA file used for embedding (required for MMseqs2 alignment)
 - **Query embeddings (npy)**: Output from the Embed Query tool
 - **Query embedding names**: Text file with sequence names from the Embed Query tool
+- **Deep search mode**: Optional flag to enable deep search, which extracts proteins from all search results instead of only aligned centroids, then aligns everything with MMseqs2
 
 **Parameters**
 
diff --git a/tools/logan_proteins/test-data/faiss_database.loc b/tools/logan_proteins/test-data/faiss_database.loc
index 2394f5c94b..a226d158fe 100644
--- a/tools/logan_proteins/test-data/faiss_database.loc
+++ b/tools/logan_proteins/test-data/faiss_database.loc
@@ -3,4 +3,4 @@
 # - db-name
 # - version
 # - /path/to/data 
-faiss-demo-db-20260203	FAISS Test Database	1.2.0	${__HERE__}/test-db/
\ No newline at end of file
+faiss-demo-db-20260203	FAISS Test Database	1.2.2	${__HERE__}/test-db/
\ No newline at end of file
diff --git a/tools/logan_proteins/tool-data/faiss_database.loc.sample b/tools/logan_proteins/tool-data/faiss_database.loc.sample
index 058761bcac..05be18eaa6 100644
--- a/tools/logan_proteins/tool-data/faiss_database.loc.sample
+++ b/tools/logan_proteins/tool-data/faiss_database.loc.sample
@@ -1,5 +1,5 @@
 #This is a sample file distributed with Galaxy that enables tools
-#to use a directory of metagenomics files.  
+#to use a directory of FAISS database files.  
 #file has this format (white space characters are TAB characters)
 # - db-build-version-date
 # - db-name
diff --git a/tools/mafft/macros.xml b/tools/mafft/macros.xml
index 3c9a44134b..cad96e4be7 100644
--- a/tools/mafft/macros.xml
+++ b/tools/mafft/macros.xml
@@ -1,6 +1,6 @@
 <macros>
     <token name="@TOOL_VERSION@">7.526</token>
-    <token name="@VERSION_SUFFIX@">2</token>
+    <token name="@VERSION_SUFFIX@">3</token>
     <token name="@PROFILE@">22.01</token>
     <!-- currently, the fasta3 executable is named according to its major version
     => needs updating together with the package requirement! -->
diff --git a/tools/mafft/mafft.xml b/tools/mafft/mafft.xml
index bb990c102c..b8c142b3fa 100644
--- a/tools/mafft/mafft.xml
+++ b/tools/mafft/mafft.xml
@@ -54,6 +54,7 @@
   ## run MAFFT with predefined MSA flavours or custom settings
   #if $flavour.type == "custom"
     mafft
+    $preservecase
     #if $flavour.guidetree.guidetree_generation == "original"
       #if $flavour.guidetree.dist_flavour.distance_method == "--6merpair"
         --6merpair
@@ -97,6 +98,7 @@
     $flavour.progressive_alignment_calculation.noscore
   #else
     $flavour.type
+    $preservecase
     #if $flavour.type == "mafft-ginsi" or "--globalpair" in str($flavour.type)
       #if $flavour.treat_unrelated_segments.unalignlevel > 0
         --allowshift --unalignlevel $flavour.treat_unrelated_segments.unalignlevel
@@ -325,6 +327,14 @@ cat $dataset >> input.fa
         </conditional>
         <param argument="--reorder" type="boolean" truevalue="--reorder" falsevalue="" checked="False" label="Reorder output?" help="Default order is input order." />
         <param argument="--treeout" type="boolean" truevalue="--treeout" falsevalue="" checked="False" label="Keep alignment tree as output?" />
+        <param name="preservecase"
+               argument="--preservecase"
+               type="boolean"
+               truevalue="--preservecase"
+               falsevalue=""
+               checked="False"
+               label="Preserve case?"
+               help="Preserve the original letter case of input sequences." />
         <param name="outputFormat" type="select" label="Output format">
             <option value="" selected="true">FASTA</option>
             <option value="--clustalout">ClustalW</option>
diff --git a/tools/rag/download_embeddings.py b/tools/rag/download_embeddings.py
index c307ded6ad..2c0302a9c5 100644
--- a/tools/rag/download_embeddings.py
+++ b/tools/rag/download_embeddings.py
@@ -1,9 +1,13 @@
+# /// script
+# requires-python = ">=3.9"
+# dependencies = ["huggingface_hub"]
+# ///
 import argparse
 import os
 import sys
 from pathlib import Path
 
-from sentence_transformers import SentenceTransformer
+from huggingface_hub import snapshot_download
 
 
 def main():
@@ -34,8 +38,7 @@ def main():
         print(f"[PATH] Destination: {out_dir}")
 
         try:
-            model = SentenceTransformer(model_id)
-            model.save(str(out_dir))
+            snapshot_download(repo_id=model_id, local_dir=str(out_dir))
             print(f"[SUCCESS] Saved {model_id}")
         except Exception as e:
             print(f"[ERROR] Could not download {model_id}: {e}")
diff --git a/tools/rag/rag_retriever.py b/tools/rag/rag_retriever.py
index ced73a6bb2..a666f26bf5 100644
--- a/tools/rag/rag_retriever.py
+++ b/tools/rag/rag_retriever.py
@@ -33,7 +33,7 @@ def main():
 
     docs: list[Document] = []
 
-    valid_file_types = ["pdf", "json", "txt", "csv", "md"]
+    valid_file_types = ["pdf", "json", "txt", "csv", "markdown"]
 
     for file_path, file_type in context_files:
         if file_type not in valid_file_types:
diff --git a/tools/rag/rag_retriever.xml b/tools/rag/rag_retriever.xml
index e39f118ee9..d3eb090133 100644
--- a/tools/rag/rag_retriever.xml
+++ b/tools/rag/rag_retriever.xml
@@ -4,7 +4,7 @@
 
   <macros>
     <token name="@TOOL_VERSION@">1.0.0</token>
-    <token name="@VERSION_SUFFIX@">0</token>
+    <token name="@VERSION_SUFFIX@">1</token>
     <token name="@CONTAINER_VERSION@">0.14.18</token>
   </macros>
 
@@ -58,7 +58,7 @@ python '$__tool_directory__/rag_retriever.py' '$context_files' '$question' '$MOD
           <options from_data_table="huggingface">
             <column name="name" index="1" />
             <column name="value" index="6" />
-            <filter type="static_value" value="embedding" column="4" />
+            <filter type="static_value" value="vector-rag" column="4" />
             <filter type="static_value" value="1" column="5" />
           </options>
           <validator type="no_options"
diff --git a/tools/rag/tool-data/huggingface.loc.sample b/tools/rag/tool-data/huggingface.loc.sample
index a67f263b72..7d6f485bee 100644
--- a/tools/rag/tool-data/huggingface.loc.sample
+++ b/tools/rag/tool-data/huggingface.loc.sample
@@ -4,9 +4,10 @@
 # <unique_build_id>	<display_name>	<pipeline_tag>	<domain>	<free_tag>	<version>	<folder_base_path>
 #
 # For this tool, embedding models can be registered here and selected via the existing
-# Galaxy "huggingface" data table.
+# Galaxy "huggingface" data table. Use free_tag=vector-rag to make models visible to
+# the RAG retriever tool.
 #
 # Example entries for embedding models:
 #
-# sentence-transformers/all-MiniLM-L6-v2	all-MiniLM-L6-v2	feature-extraction	text	embedding	1	/path/to/huggingface_models/sentence-transformers/all-MiniLM-L6-v2
-# BAAI/bge-small-en	BAAI bge-small-en	feature-extraction	text	embedding	1	/path/to/huggingface_models/BAAI/bge-small-en
\ No newline at end of file
+# sentence-transformers/all-MiniLM-L6-v2	all-MiniLM-L6-v2	feature-extraction	text	vector-rag	1	/path/to/huggingface_models/sentence-transformers/all-MiniLM-L6-v2
+# BAAI/bge-small-en	BAAI bge-small-en	feature-extraction	text	vector-rag	1	/path/to/huggingface_models/BAAI/bge-small-en
\ No newline at end of file
diff --git a/tools/rna_tools/ribotaper/macros.xml b/tools/rna_tools/ribotaper/macros.xml
index 4ac71c28ad..2e00e4be53 100644
--- a/tools/rna_tools/ribotaper/macros.xml
+++ b/tools/rna_tools/ribotaper/macros.xml
@@ -1,11 +1,11 @@
 <macros>
-    <token name="@TOOL_VERSION@">1.3.1a</token>
-    <token name="@VERSION_SUFFIX@">2</token>
+    <token name="@TOOL_VERSION@">1.3.1</token>
+    <token name="@VERSION_SUFFIX@">0</token>
     <xml name="requirements">
         <requirements>
             <requirement type="package" version="@TOOL_VERSION@">ribotaper</requirement>
-            <requirement type="package" version="9.1">coreutils</requirement>
-            <requirement type="package" version="9.54.0">ghostscript</requirement>
+            <requirement type="package" version="9.5">coreutils</requirement>
+            <requirement type="package" version="10.07.0">ghostscript</requirement>
 
         </requirements>
     </xml>
diff --git a/tools/rna_tools/ribotaper/ribotaper_part1_create_annotation_files.xml b/tools/rna_tools/ribotaper/ribotaper_part1_create_annotation_files.xml
index d39ba3bbf1..4009889695 100644
--- a/tools/rna_tools/ribotaper/ribotaper_part1_create_annotation_files.xml
+++ b/tools/rna_tools/ribotaper/ribotaper_part1_create_annotation_files.xml
@@ -26,7 +26,7 @@
 
     ]]></command>
     <inputs>
-        <param name="gtf" type="data" format="GTF" label="Annotation file"
+        <param name="gtf" type="data" format="gtf" label="Annotation file"
             help="The GTF file should contain: 1) coding and non-coding genes, 2) a 'transcript_id' and a 'gene_id' field for each 'exon' and 'CDS' row."/>
         <conditional name="reference_genome">
             <param name="source" type="select" label="Source for the genome" help="Built-in references were created using default options.">
diff --git a/tools/rna_tools/ribotaper/ribotaper_part3_main.xml b/tools/rna_tools/ribotaper/ribotaper_part3_main.xml
index 0404c93a00..d37285c24b 100644
--- a/tools/rna_tools/ribotaper/ribotaper_part3_main.xml
+++ b/tools/rna_tools/ribotaper/ribotaper_part3_main.xml
@@ -8,8 +8,8 @@
         <exit_code range="1:" />
     </stdio>
     <command><![CDATA[
-        #if $annotation_path.is_of_type("tgz")
-            tar -xzvf '${annotation_path}' &&
+        #if $annotation_path.is_of_type("tar.gz")
+            tar -xvzf '${annotation_path}' &&
         #else
              tar -xvf '${annotation_path}' &&
         #end if
@@ -22,9 +22,9 @@
             \${GALAXY_SLOTS:-12}
     ]]></command>
     <inputs>
-        <param name="annotation_path" type="data" format="tgz,tar" label="Annotation path" help="Please run 'ribotaper part 1' to generate the archive."/>
-        <param name="ribo_bam" type="data" format="BAM" label="Ribo-seq alignment file" help="Ribo-seq alignment file in BAM format."/>
-        <param name="rna_bam" type="data" format="BAM" label="RNA-seq alignment file" help="RNA-seq alignment file in BAM format."/>
+        <param name="annotation_path" type="data" format="tar.gz,tgz,tar" label="Annotation path" help="Please run 'ribotaper part 1' to generate the archive."/>
+        <param name="ribo_bam" type="data" format="bam" label="Ribo-seq alignment file" help="Ribo-seq alignment file in BAM format."/>
+        <param name="rna_bam" type="data" format="bam" label="RNA-seq alignment file" help="RNA-seq alignment file in BAM format."/>
         <param name="read_lenghts_ribo" type="text" value="26,28,29"  label="Read length" help="Read lengths, comma-separated values, which are used for P-site calculation. Example, 26,28,29.
             Please run 'ribotaper part 2' to deterimine appropriate values.">
             <sanitizer invalid_char="">
@@ -55,6 +55,12 @@
         <data name="output8" format="pdf" from_work_dir="Final_ORF_results.pdf" label="${tool.name} on ${on_string}: ORF categories (length/coverage)"/>
     </outputs>
     <tests>
+        <test expect_num_outputs="8">
+            <param name="annotation_path" value="annotation_path.tgz" ftype="tar.gz"/>
+            <param name="ribo_bam" value="test_ribo.bam"/>
+            <param name="rna_bam" value="test_rna.bam"/>
+            <output name="output2" file="ORFs_genes_found"/>
+        </test>
         <test expect_num_outputs="8">
             <param name="annotation_path" value="annotation_path.tgz"/>
             <param name="ribo_bam" value="test_ribo.bam"/>
diff --git a/tools/rna_tools/sortmerna/macros.xml b/tools/rna_tools/sortmerna/macros.xml
index cb8a3d2173..2e1ecac083 100644
--- a/tools/rna_tools/sortmerna/macros.xml
+++ b/tools/rna_tools/sortmerna/macros.xml
@@ -1,5 +1,5 @@
 <macros>
-    <token name="@TOOL_VERSION@">4.4.0</token>
+    <token name="@TOOL_VERSION@">5.0.0</token>
     <token name="@VERSION_SUFFIX@">0</token>
     <xml name="biotools">
         <xrefs>
diff --git a/tools/tiara/macros.xml b/tools/tiara/macros.xml
index ced8daa721..bc0eed5e16 100644
--- a/tools/tiara/macros.xml
+++ b/tools/tiara/macros.xml
@@ -1,10 +1,10 @@
 <macros>
     <token name="@TOOL_VERSION@">1.0.3</token>
-    <token name="@VERSION_SUFFIX@">galaxy0</token>
+    <token name="@VERSION_SUFFIX@">2</token>
+    <token name="@PROFILE@">25.1</token>
     <xml name="requirements">
         <requirements>
             <requirement type="package" version="@TOOL_VERSION@">tiara</requirement>
-            <requirement type="package" version="3.8">python</requirement>
         </requirements>
     </xml>
     <xml name="biotools">
diff --git a/tools/tiara/tiara.xml b/tools/tiara/tiara.xml
index d272929edb..e942a7f01c 100644
--- a/tools/tiara/tiara.xml
+++ b/tools/tiara/tiara.xml
@@ -1,4 +1,4 @@
-<tool id="tiara" name="tiara" version="@TOOL_VERSION@+galaxy1" profile="21.05">
+<tool id="tiara" name="tiara" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
     <description>Deep-learning-based approach for identification of eukaryotic sequences in the metagenomic data </description>
     <macros>
         <import>macros.xml</import>
@@ -6,11 +6,12 @@
     <expand macro="biotools"/>
     <expand macro="requirements"/>
     <command detect_errors="exit_code"><![CDATA[ 
-        mkdir ./results/ &&
+        mkdir -p ./txt &&
+
         tiara 
         -t \${GALAXY_SLOTS:-4} 
         -i '$input' 
-        -o ./results/main_result.txt
+        -o ./txt/main_result.txt
 
         #if $probabilities
             --pr '$probabilities'
@@ -28,26 +29,33 @@
             --k1 $advanced_options.advance.first_stage_kmer
             --k2 $advanced_options.advance.second_stage_kmer
         #end if
-        #if $taxonomy_filter
-            --tf #for $tf in $taxonomy_filter
+        #if $fasta_output.produce_fasta == "yes"
+            --tf #for $tf in $fasta_output.taxonomy_filter
                 $tf
             #end for
-            #for $tf in $taxonomy_filter
-              && ls -l ./results/
-              &&  mv ./results/${tf}*.dat ./results/${tf}.fasta
-            #end for
         #end if
 
     ]]></command>
     <inputs>
         <param name="input" type="data" format="fasta" label="input fasta,fasta.gz file"/>
-        <param name="taxonomy_filter" type="select" multiple="true" optional="true" label="Write sequences to fasta,fasta.gz files specified in the arguments to this option." help="all refers to all classes present in input fasta (to separate fasta files).">
-            <option value="mit">mitochondria</option>
-            <option value="pla">plastid</option>
-            <option value="bac">bacteria</option>
-            <option value="arc">archea</option>
-            <option value="euk">eukarya</option>
-        </param>
+        <conditional name="fasta_output">
+            <param name="produce_fasta" type="select" label="Produce split FASTA output?" help="Select Yes to write classified sequences for selected groups as separate FASTA outputs. By default, no FASTA files are produced and only the main classification table and log are generated.">
+                <option value="no" selected="true">No</option>
+                <option value="yes">Yes</option>
+            </param>
+            <when value="yes">
+                <param name="taxonomy_filter" type="select" multiple="true" label="Select sequence types">
+                    <option value="mit">mitochondria</option>
+                    <option value="pla">plastid</option>
+                    <option value="bac">bacteria</option>
+                    <option value="arc">archaea</option>
+                    <option value="euk">eukarya</option>
+                    <option value="unk">unknown</option>
+                </param>
+            </when>
+            <when value="no"/>
+        </conditional>
+
         <param argument="probabilities" type="boolean" truevalue="--pr" falsevalue="" checked="false" label="Add probabilities of individual classes for each sequence."/>
         <param argument="min_len" type="integer" value="3000" min="1000" optional="true" label="Minimum length of a sequence. Default: 3000 bp." help="Specify the desired minimum length in base pairs.Default value is 3000 bp and we do not recommend classifying sequences shorter than 1000 bp. "/>
         <param argument="cutoff_stage1" type="float" value="0.65" min="0.5" max="1" optional="true" label="Probability threshold for the first stage." help="Probability threshold needed for classification in the first stage. Default: 0.65." />
@@ -78,40 +86,61 @@
         </section>
     </inputs>
     <outputs>
-        <collection name="output" type="list" label="${tool.name} on ${on_string}: classified sequences in txt and Fasta Output">
-            <discover_datasets pattern="__name_and_ext__"  ext="fasta,txt" directory="results" />
+        <collection name="output_fasta" type="list" label="${tool.name} on ${on_string}: Fasta Output">
+            <filter>fasta_output['produce_fasta'] == 'yes'</filter>
+            <discover_datasets pattern="(?P&lt;designation&gt;[^_]+)_dataset_.*\.dat$"  format="fasta" directory="txt" />
         </collection>
+        <data name="main_result" format="tabular" from_work_dir="txt/main_result.txt" label="${tool.name} on ${on_string}: main result" />
+        <data name="log_result" format="txt" from_work_dir="txt/log_main_result.txt" label="${tool.name} on ${on_string}: log" />
     </outputs>
     <tests>
-        <test expect_num_outputs="1">
+        <test expect_num_outputs="3">
             <param name="input" value="plast_fr.fasta.gz"/>
-            <param name="taxonomy_filter" value="pla"/>
-            <output_collection name="output" type="list">
-                <element name="main_result" file="main_result01.txt" ftype="txt"/>
-                <element name="pla" file="pla" ftype="fasta" />
+            <param name="fasta_output|produce_fasta" value="yes"/>
+            <param name="fasta_output|taxonomy_filter" value="pla"/>
+            <output_collection name="output_fasta" type="list">
+                <element name="plastid" file="pla" ftype="fasta" />
             </output_collection>
+            <output name="main_result" file="main_result01.txt" ftype="tabular" />
+            <output name="log_result" ftype="txt">
+                <assert_contents>
+                    <has_text text="First iteration statistics" />
+                </assert_contents>
+            </output>
         </test>
-        <test expect_num_outputs="1">
+        <test expect_num_outputs="3">
             <param name="input" value="sample_all.fasta"/>
-            <param name="taxonomy_filter" value="euk,bac,arc"/>
-            <output_collection name="output" type="list">
-                <element name="arc" file="arc" ftype="fasta" />
-                <element name="bac" file="bac" ftype="fasta" />
-                <element name="euk" file="euk" ftype="fasta" />
-                <element name="main_result" file="main_result02.txt" ftype="txt" />
+            <param name="fasta_output|produce_fasta" value="yes"/>
+            <param name="fasta_output|taxonomy_filter" value="euk,bac,arc,unk"/>
+            <output_collection name="output_fasta" type="list">
+                <element name="archaea" file="arc" ftype="fasta" />
+                <element name="bacteria" file="bac" ftype="fasta" />
+                <element name="eukarya" file="euk" ftype="fasta" />
             </output_collection>
+            <output name="main_result" file="main_result02.txt" ftype="tabular" />
+            <output name="log_result" ftype="txt">
+                <assert_contents>
+                    <has_text text="Models used:" />
+                </assert_contents>
+            </output>
         </test>
-        <test expect_num_outputs="1">
+        <test expect_num_outputs="3">
             <param name="input" value="eukarya_fr.fasta"/>
-            <param name="taxonomy_filter" value="euk"/>
+            <param name="fasta_output|produce_fasta" value="yes"/>
+            <param name="fasta_output|taxonomy_filter" value="euk"/>
             <param name="min_len" value="5000"/>
             <param name="cutoff_stage1" value="0.65"/>
             <param name="cutoff_stage2" value="0.60"/>
             <param name="probabilities" value="true"/>
-            <output_collection name="output" type="list">
-                <element name="euk" file="euk" ftype="fasta" />
-                <element name="main_result" file="main_result03.txt" ftype="txt" />
+            <output_collection name="output_fasta" type="list">
+                <element name="eukarya" file="euk" ftype="fasta" />
             </output_collection>
+            <output name="main_result" file="main_result03.txt" ftype="tabular" />
+            <output name="log_result" ftype="txt">
+                <assert_contents>
+                    <has_text text="Hyperparameters:" />
+                </assert_contents>
+            </output>
         </test>
     </tests>
     <help><![CDATA[
diff --git a/tools/webatlas/.shed.yml b/tools/webatlas/.shed.yml
new file mode 100644
index 0000000000..dca0dc92c2
--- /dev/null
+++ b/tools/webatlas/.shed.yml
@@ -0,0 +1,16 @@
+name: webatlas
+owner: iuc
+description: The Galaxy WebAtlas tools to process spatial and single-cell experiment data for visualisation in a web browser using Vitessce.
+homepage_url: https://github.com/haniffalab/webatlas-pipeline
+long_description: The Galaxy WebAtlas tools provide a framework for processing spatial and single-cell experiment data, enabling visualisation with Vitessce.
+remote_repository_url: https://github.com/bgruening/galaxytools/tree/master/tools/webatlas
+categories:
+- Spatial Omics
+- Single Cell
+auto_tool_repositories:
+  name_template: "{{ tool_id }}"
+  description_template: "Wrapper for {{ tool_name }}."
+suite:
+  name: "suite_webatlas"
+  description: "A suite of Galaxy tools to process single-cell and spatial experiment data for visualisation using Vitessce."
+  type: repository_suite_definition
\ No newline at end of file
diff --git a/tools/webatlas/build_config.xml b/tools/webatlas/build_config.xml
new file mode 100644
index 0000000000..303573d80a
--- /dev/null
+++ b/tools/webatlas/build_config.xml
@@ -0,0 +1,449 @@
+<tool id="webatlas_build_config" name="WebAtlas Build Vitessce Config" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE_VERSION@">
+    <description>from AnnData and image Zarr inputs</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements"/>
+    <command detect_errors="exit_code"><![CDATA[
+        cat $images_script &&
+        python '$images_script' &&
+        cat $options_script &&
+        python '$options_script' &&
+        build_config.py
+        --project '$project'
+        --dataset '$dataset'
+        --file_paths '["/api/datasets/${__app__.security.encode_id($input_file_path.id)}/extra_files/raw/$input_file_path.metadata.store_root/"]'
+        --images "\$(cat images.json)"
+        --url '${__app__.config.galaxy_infrastructure_url}'
+        --options "\$(cat options.json)"
+        --layout '$layout'
+        #if $custom_layout:
+            --custom_layout '$custom_layout'
+        #end if
+        #if $title:
+            --title '$title'
+        #end if
+        #if $description:
+            --description '$description'
+        #end if
+        #if $config_filename_suffix:
+            --config_filename_suffix '$config_filename_suffix'
+        #end if
+        &&
+        mv '${project}-${dataset}-${config_filename_suffix}'* '$output_json'
+    ]]></command>
+<configfiles>
+<configfile name="images_script"><![CDATA[
+import json
+
+images = {"raw": [], "label": []}
+
+#if $sec_label_img.input_image_label and $sec_label_img.input_metadata_label and $sec_label_img.image_name_label
+label_zarr_path = "/api/datasets/${__app__.security.encode_id($sec_label_img.input_image_label.id)}/extra_files/raw/${sec_label_img.input_image_label.metadata.store_root}/"
+label_metadata_path = "${sec_label_img.input_metadata_label}"
+label_image_name = "${sec_label_img.image_name_label}"
+
+with open(label_metadata_path) as md_file:
+    label_md = json.load(md_file)
+
+images["label"].append({
+    "path": label_zarr_path,
+    "name": f"{label_image_name}-label",
+    "md": label_md
+})
+#end if
+
+#if $sec_raw_img.input_image_raw and $sec_raw_img.input_metadata_raw and $sec_raw_img.image_name_raw
+raw_zarr_path = "/api/datasets/${__app__.security.encode_id($sec_raw_img.input_image_raw.id)}/extra_files/raw/${sec_raw_img.input_image_raw.metadata.store_root}/"
+raw_metadata_path = "${sec_raw_img.input_metadata_raw}"
+raw_image_name = "${sec_raw_img.image_name_raw}"
+
+with open(raw_metadata_path) as md_file:
+    raw_md = json.load(md_file)
+
+images["raw"].append({
+    "path": raw_zarr_path,
+    "name": f"{raw_image_name}-raw",
+    "md": raw_md
+})
+#end if
+
+clean_dict = {}
+for key, value in images.items():
+    if value:
+        clean_dict[key] = value
+images = clean_dict
+
+with open("images.json", "w") as file:
+    json.dump(images, file)
+]]>
+</configfile>
+<configfile name="options_script"><![CDATA[
+import json
+
+options = {}
+
+spatial = "${sec_vitessce_options.spatial}".strip()
+factors= "${sec_vitessce_options.factors}".strip()
+sets = "${sec_vitessce_options.sets}".strip()
+matrix = "${sec_vitessce_options.matrix}".strip()
+
+## spatial
+if spatial:
+    options["spatial"] = {
+        "xy": f"obsm/{spatial}"
+    }
+
+## mappings
+mappings = {}
+
+#if $sec_vitessce_options.sec_mappings_spatial.mappings_spatial == "true" and $sec_vitessce_options.spatial:
+spatial_dim1 = "${sec_vitessce_options.sec_mappings_spatial.spatial_dim1}"
+spatial_dim2 = "${sec_vitessce_options.sec_mappings_spatial.spatial_dim2}"
+if spatial_dim1 != "" and spatial_dim2 != "":
+    mappings[f"obsm/{spatial}"] = [int(spatial_dim1), int(spatial_dim2)]
+#end if
+
+#if $sec_vitessce_options.sec_mappings_pca.pca_value:
+pca_value = "${sec_vitessce_options.sec_mappings_pca.pca_value}"
+pca_dim1 = "${sec_vitessce_options.sec_mappings_pca.pca_dim1}"
+pca_dim2 = "${sec_vitessce_options.sec_mappings_pca.pca_dim2}"
+if pca_dim1 != "" and pca_dim2 != "":
+    mappings[f"obsm/{pca_value}"] = [int(pca_dim1), int(pca_dim2)]
+#end if
+
+#if $sec_vitessce_options.sec_mappings_umap.umap_value:
+umap_value = "${sec_vitessce_options.sec_mappings_umap.umap_value}"
+umap_dim1 = "${sec_vitessce_options.sec_mappings_umap.umap_dim1}"
+umap_dim2 = "${sec_vitessce_options.sec_mappings_umap.umap_dim2}"
+if umap_dim1 != "" and umap_dim2 != "":
+    mappings[f"obsm/{umap_value}"] = [int(umap_dim1), int(umap_dim2)]
+#end if
+
+if mappings:
+    options["mappings"] = mappings
+
+## factors
+if factors:
+    options["factors"] = [f"obs/{f.strip()}" for f in factors.split(",") if f.strip()]
+
+## sets
+if sets:
+    parsed_sets = []
+
+    for s in sets.split(","):
+        s = s.strip()
+        if not s:
+            continue
+
+        if ":" in s:
+            name, score = [x.strip() for x in s.split(":", 1)]
+            parsed_sets.append({"name": f"obs/{name}","score": f"obs/{score}"})
+        else:
+            parsed_sets.append(f"obs/{s}")
+    if parsed_sets:
+        options["sets"] = parsed_sets
+
+## matrix
+if matrix:
+    options["matrix"] = matrix
+
+with open("options.json", "w") as file:
+    json.dump(options, file, indent=2)
+]]>
+</configfile>
+</configfiles>
+    <inputs>
+        <param name="input_file_path" type="data" format="zarr" label="AnnData Zarr generated by WebAtlas Process files"/>
+        <section name="sec_label_img" title="Add label image">
+            <param name="input_image_label" type="data" optional="true" format="zarr" label="Image Zarr generated by WebAtlas Consolidate Metadata"/>
+            <param name="input_metadata_label" type="data" optional="true" format="json" label="Metadata JSON generated by WebAtlas OME Zarr Metadata"/>
+            <param name="image_name_label" type="text" optional="true" label="Image name (prefix)" help="Display name prefix used inside Vitessce. Should be the same as the 'prefix' used in other WebAtlas tools. E.g. 'visium-breast-cancer'.">
+                <expand macro="sanitizer_prefix"/>
+            </param>
+        </section>
+        <section name="sec_raw_img" title="Add raw image">
+            <param name="input_image_raw" type="data" optional="true" format="zarr" label="Image Zarr generated by WebAtlas Consolidate Metadata"/>
+            <param name="input_metadata_raw" type="data" optional="true" format="json" label="Metadata JSON generated by WebAtlas OME Zarr Metadata"/>
+            <param name="image_name_raw" type="text" optional="true" label="Image name (prefix)" help="Display name prefix used inside Vitessce. Should be the same as the 'prefix' used in other WebAtlas tools. E.g. 'visium-breast-cancer'.">
+                <expand macro="sanitizer_prefix"/>
+            </param>
+        </section>
+        <param name="project" type="text" value="project" optional="false" label="Project name" help="Displayed in the config metadata and used in the output filename.">
+            <expand macro="sanitizer_prefix"/>
+        </param>
+        <param name="dataset" type="text" value="dataset" optional="false" label="Dataset name" help="Displayed in the config metadata and used in the output filename.">
+            <expand macro="sanitizer_prefix"/>
+        </param>
+        <param argument="--layout" type="select" label="Layout" help="Predefined Vitessce layout to use. Default: minimal.">
+            <option value="minimal" selected="true">minimal</option>
+            <option value="simple">simple</option>
+            <option value="advanced">advanced</option>
+        </param>
+        <section name="sec_vitessce_options" title="Vitessce config file options">
+            <param name="spatial" type="text" value="spatial" label="Where the AnnData object stores the spatial coordinates" help="Examples: 'spatial', 'X_spatial'. 'xy: obsm/' gets prepended automatically.">
+                <expand macro="sanitizer_options"/>
+            </param>
+            <section name="sec_mappings_spatial" title="Spatial mapping">
+                <param name="mappings_spatial" type="boolean" checked="false" optional="true" label="Include spatial in scatterplot" help="Provide values for the following 2 dimensions if you choose 'Yes' here."/>
+                <param name="spatial_dim1" type="integer" value="" optional="true" label="Spatial dimension 1" help="Dimension to be plotted on the x-axis."/>
+                <param name="spatial_dim2" type="integer" value="" optional="true" label="Spatial dimension 2" help="Dimension to be plotted on the y-axis."/>
+            </section>
+            <section name="sec_mappings_pca" title="PCA mapping">
+                <param name="pca_value" type="text" value="" optional="true" label="Where the PCA is stored" help="Includes PCA in scatterplot. Example: 'X_pca'. 'obsm/' gets prepended automatically. Provide values for the following 2 dimensions if enter a value here.">
+                    <expand macro="sanitizer_options"/>
+                </param>
+                <param name="pca_dim1" type="integer" value="" optional="true" label="PCA dimension 1" help="Dimension to be plotted on the x-axis(e.g. PC1)"/>
+                <param name="pca_dim2" type="integer" value="" optional="true" label="PCA dimension 2" help="Dimension to be plotted on the y-axis(e.g. PC2)"/>
+            </section>
+            <section name="sec_mappings_umap" title="UMAP mapping">
+                <param name="umap_value" type="text" value="" optional="true" label="Where the UMAP is stored" help="Includes UMAP in scatterplot. Example: 'X_umap'. 'obsm/' gets prepended automatically. Provide values for the following 2 dimensions if you enter a value here.">
+                    <expand macro="sanitizer_options"/>
+                </param>
+                <param name="umap_dim1" type="integer" value="" optional="true" label="UMAP dimension 1" help="Dimension to be plotted on the x-axis."/>
+                <param name="umap_dim2" type="integer" value="" optional="true" label="UMAP dimension 2" help="Dimension to be plotted on the y-axis."/>
+            </section>
+            <param name="factors" type="text"  value="" optional="true" label="Factors" help="Comma-separated list of 'obs' fields to show when hovering over cells in the visualization. Example input: sample. 'obs/' gets prepended automatically.">
+                <sanitizer invalid_char="">
+                    <valid initial="string.ascii_letters,string.digits">
+                        <add value="_"/>
+                        <add value="-"/>
+                        <add value="."/>
+                        <add value=","/>
+                    </valid>
+                </sanitizer>
+            </param>
+            <param name="sets" type="text" value="" optional="true" label="Sets" help="Comma-separated list of keys for grouping cells. Use 'name' for simple sets or 'name:score' for scored sets. Example: 'cluster, celltype:celltype_prob'.">
+                <sanitizer invalid_char="">
+                    <valid initial="string.ascii_letters,string.digits">
+                        <add value="_"/>
+                        <add value="-"/>
+                        <add value="."/>
+                        <add value=","/>
+                        <add value=":"/>
+                        <add value=" "/>
+                    </valid>
+                </sanitizer>
+            </param>
+            <param name="matrix" type="text" value="X" optional="true" label="Matrix" help="Expression matrix to use in the Vitessce config. Default: X.">
+                <expand macro="sanitizer_options"/>
+            </param>
+        </section>
+        <section name="sec_advanced_options" title="Advanced options" expanded="false">
+            <param argument="--title" type="text" value="" optional="true" label="Title" help="Data title to show in the visualization.">
+                <expand macro="sanitizer_printable"/>
+            </param>
+            <param argument="--description" type="text" value="" optional="true" label="Description" help="Description to include in the config file.">
+                <expand macro="sanitizer_printable"/>
+            </param>
+            <param argument="--config_filename_suffix" type="text" value="config.json" optional="true" label="Config filename suffix" help="Default value: config.json">
+                <expand macro="sanitizer_options"/>
+            </param>
+            <param argument="--custom_layout" type="text" value="" optional="true" label="Custom layout" help="Text defining a Vitessce layout following its alternative syntax. See tool help section for more details.">
+                <expand macro="sanitizer_printable"/>
+            </param>
+        </section>
+    </inputs>
+    <outputs>
+        <data name="output_json" format="vitessce.json" label="${tool.name} on ${on_string}: $project-$dataset-$config_filename_suffix"/>
+    </outputs>
+    <tests>
+    <test expect_num_outputs="1">
+        <param name="input_file_path" location="https://zenodo.org/records/20029977/files/visium-breast-cancer-anndata.zarr.zip"/>
+        <param name="project" value="visium"/>
+        <param name="dataset" value="breast-cancer"/>
+        <section name="sec_label_img">
+            <param name="input_image_label" location="https://zenodo.org/records/20029977/files/visium-breast-cancer-label.zarr.zip"/>
+            <param name="input_metadata_label" location="https://zenodo.org/records/20029977/files/metadata_label.json"/>
+            <param name="image_name_label" value="visium-breast-cancer"/>
+        </section>
+        <section name="sec_raw_img">
+            <param name="input_image_raw" location="https://zenodo.org/records/20029977/files/visium-breast-cancer-raw.zarr.zip"/>
+            <param name="input_metadata_raw" location="https://zenodo.org/records/20029977/files/metadata_raw.json"/>
+            <param name="image_name_raw" value="visium-breast-cancer"/>
+        </section>
+        <param name="layout" value="advanced"/>
+        <section name="sec_advanced_options">
+            <param name="title" value="Visium CytAssist - High resolution mapping of the breast cancer tumor microenvironment"/>
+            <param name="description" value="test description"/>
+        </section>
+        <output name="output_json">
+            <assert_contents>
+                <has_json_property_with_text property="name" text="Visium CytAssist - High resolution mapping of the breast cancer tumor microenvironment"/>
+                <has_json_property_with_text property="description" text="test description"/>
+                <has_json_property_with_text property="uid" text="breast-cancer"/>
+                <has_json_property_with_text property="name" text="breast-cancer"/>
+                <has_json_property_with_text property="fileType" text="raster.json"/>
+                <has_json_property_with_text property="name" text="visium-breast-cancer-raw"/>
+                <has_json_property_with_text property="name" text="visium-breast-cancer-label"/>
+                <has_json_property_with_text property="fileType" text="anndata.zarr"/>
+                <has_json_property_with_text property="path" text="obsm/spatial"/>
+                <has_json_property_with_text property="path" text="X"/>
+                <has_size value="4274" delta="300"/>
+            </assert_contents>
+        </output>
+    </test>
+
+    <test expect_num_outputs="1">
+        <param name="input_file_path" location="https://zenodo.org/records/20029977/files/visium-breast-cancer-anndata.zarr.zip"/>
+        <param name="project" value="visium"/>
+        <param name="dataset" value="breast-cancer"/>
+        <section name="sec_label_img">
+            <param name="input_image_label" location="https://zenodo.org/records/20029977/files/visium-breast-cancer-label.zarr.zip"/>
+            <param name="input_metadata_label" location="https://zenodo.org/records/20029977/files/metadata_label.json"/>
+            <param name="image_name_label" value="visium-breast-cancer"/>
+        </section>
+        <section name="sec_advanced_options">
+            <param name="title" value="Visium CytAssist - High resolution mapping of the breast cancer tumor microenvironment"/>
+            <param name="description" value="test description"/>
+        </section>
+        <output name="output_json">
+            <assert_contents>
+                <has_json_property_with_text property="name" text="Visium CytAssist - High resolution mapping of the breast cancer tumor microenvironment"/>
+                <has_json_property_with_text property="description" text="test description"/>
+                <has_json_property_with_text property="uid" text="breast-cancer"/>
+                <has_json_property_with_text property="name" text="breast-cancer"/>
+                <has_json_property_with_text property="fileType" text="raster.json"/>
+                <has_json_property_with_text property="name" text="visium-breast-cancer-label"/>
+                <has_json_property_with_text property="fileType" text="anndata.zarr"/>
+                <has_json_property_with_text property="path" text="obsm/spatial"/>
+                <has_json_property_with_text property="path" text="X"/>
+                <has_size value="2581" delta="300"/>
+            </assert_contents>
+        </output>
+    </test>
+
+    <test expect_num_outputs="1">
+        <param name="input_file_path" location="https://zenodo.org/records/20029977/files/visium-breast-cancer-anndata.zarr.zip"/>
+        <param name="project" value="visium"/>
+        <param name="dataset" value="breast-cancer"/>
+        <section name="sec_raw_img">
+            <param name="input_image_raw" location="https://zenodo.org/records/20029977/files/visium-breast-cancer-raw.zarr.zip"/>
+            <param name="input_metadata_raw" location="https://zenodo.org/records/20029977/files/metadata_raw.json"/>
+            <param name="image_name_raw" value="visium-breast-cancer"/>
+        </section>
+        <param name="layout" value="simple"/>
+        <section name="sec_advanced_options">
+            <param name="title" value="Visium CytAssist - High resolution mapping of the breast cancer tumor microenvironment"/>
+            <param name="description" value="test description"/>
+        </section>
+        <output name="output_json">
+            <assert_contents>
+                <has_json_property_with_text property="name" text="Visium CytAssist - High resolution mapping of the breast cancer tumor microenvironment"/>
+                <has_json_property_with_text property="description" text="test description"/>
+                <has_json_property_with_text property="uid" text="breast-cancer"/>
+                <has_json_property_with_text property="name" text="breast-cancer"/>
+                <has_json_property_with_text property="fileType" text="raster.json"/>
+                <has_json_property_with_text property="name" text="visium-breast-cancer-raw"/>
+                <has_json_property_with_text property="fileType" text="anndata.zarr"/>
+                <has_json_property_with_text property="path" text="obsm/spatial"/>
+                <has_json_property_with_text property="path" text="X"/>
+                <has_size value="2820" delta="300"/>
+            </assert_contents>
+        </output>
+    </test>
+    </tests>
+    <help><![CDATA[
+This tool generates a Vitessce view configuration file (JSON) for visualizing single cell and spatial omics data in Galaxy.
+
+It combines processed AnnData, image data, and their metadata, produced by upstream WebAtlas tools, into a unified configuration that can be opened directly in the Vitessce viewer.
+
+----
+
+**Inputs**
+
+- **AnnData Zarr**
+  generated by *WebAtlas Process Files*
+
+- **Label image Zarr** *(optional)*
+  generated by *WebAtlas Consolidate Metadata*
+
+- **Label metadata JSON** *(optional)*
+  generated by *WebAtlas OME Zarr Metadata*
+
+- **Raw image Zarr** *(optional)*
+  generated by *WebAtlas Consolidate Metadata*
+
+- **Raw metadata JSON** *(optional)*
+  generated by *WebAtlas OME Zarr Metadata*
+
+Label and raw image inputs are optional and can be provided independently.
+
+----
+
+**Layout Options**
+
+The layout determines which visualization panels are shown in Vitessce.
+
+- **Minimal**
+  Spatial view and layer controller.
+
+- **Simple**
+  Extends the minimal layout by adding feature list and observation sets panels.
+  Enables exploration of gene expression and grouping of observations.
+
+- **Advanced**
+  Includes spatial view, layer controller, scatter plot, observation sets,
+  feature list, and genomic profiles panels.
+
+Panels not supported by the provided data are automatically hidden.
+
+Alternatively, a custom layout can be defined. See below for details.
+
+----
+
+**Vitessce Options**
+
+- **Spatial coordinates**
+  Location of spatial coordinates in the AnnData (e.g. *obsm/spatial*)
+
+- **Embeddings mapping**
+  Configure embeddings (e.g. spatial, PCA, UMAP) for scatter plots.
+  Define which dimensions are used for the x- and y-axis for each embedding.
+
+- **Factors**
+  Observation annotations displayed when hovering over cells.
+
+- **Sets**
+  Group observations into sets (e.g. clusters or cell types).
+  Supports scored sets (e.g. *celltype:probability*).
+
+- **Matrix**
+  Expression matrix used for visualization (e.g. *X* in the AnnData).
+
+----
+
+**Custom Layout**
+
+A custom Vitessce layout can be defined, replacing the predefined layout.
+Layout determines which visualization panels are shown in Vitessce.
+
+Syntax:
+    - Possible panels (case sensitive!): spatial, layerController, scatterplot,
+      featureList, obsSets, genomicProfiles
+    - Use "|" for left-to-right layout
+    - Use "/" for top-to-bottom layout
+    - Use parentheses for grouping
+
+Example inputs:
+    - spatial|layerController
+    - spatial|(layerController/(featureList|obsSets))
+    - layerController|spatial|((scatterplot/obsSets)|featureList)
+
+Notes:
+    - If a custom layout is provided, it overrides the predefined layout option.
+    - Panels not supported by the provided data (e.g. scatterplot without embeddings) are automatically hidden.
+    - Invalid panel identifiers are ignored or can lead to the tool failing.
+    - If the final expression is invalid, config generation may fail.
+
+----
+
+**Output**
+
+- **Vitessce configuration (JSON)**
+
+The output can be opened directly in Galaxy by clicking the **View** button in the history,
+which launches the integrated Vitessce visualization.
+    ]]></help>
+    <expand macro="citations"/>
+</tool>
\ No newline at end of file
diff --git a/tools/webatlas/consolidate_md.xml b/tools/webatlas/consolidate_md.xml
new file mode 100644
index 0000000000..1618c7e01b
--- /dev/null
+++ b/tools/webatlas/consolidate_md.xml
@@ -0,0 +1,98 @@
+<tool id="webatlas_consolidate_md" name="WebAtlas Consolidate Metadata" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" python_template_version="3.5" profile="@PROFILE_VERSION@">
+    <description>Converts an image to Zarr and consolidates metadata</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements"/>
+    <command detect_errors="exit_code"><![CDATA[
+        if tiffinfo '$input_image' | grep 'Compression Scheme:' | grep -wq 'JPEG';
+        then
+            if od -h -j2 -N2 '$input_image' | head -n1 | sed 's/[0-9]*  *//' | grep -q -E '002b|2b00';
+            then
+                tiffcp -c none -m 0 -8 '$input_image' uncompressed.tiff;
+            else
+                tiffcp -c none -m 0 '$input_image' uncompressed.tiff || tiffcp -c none -m 0 -8 '$input_image' uncompressed.tiff;
+            fi;
+                bioformats2raw --no-hcs uncompressed.tiff '$stem-$image_type'.zarr;
+        else
+            bioformats2raw --no-hcs '$input_image' '$stem-$image_type'.zarr;
+        fi;
+        consolidate_md.py --file_in '$stem-$image_type'.zarr &&
+        mkdir -p '$output_zarr.extra_files_path' &&
+        mv '$stem-$image_type'.zarr '$output_zarr.extra_files_path'
+    ]]></command>
+    <inputs>
+        <param name="input_image" type="data" format="tif,tiff,jpg" label="TIFF or JPEG image" help="Input image to convert to Zarr. JPEG-compressed TIFF images are automatically decompressed before conversion."/>
+        <expand macro="stem"/>
+        <param name="image_type" type="select" label="Input image type" help="Choose the type of input image.">
+            <option value="label">label</option>
+            <option value="raw">raw</option>
+        </param>
+    </inputs>
+    <outputs>
+        <data name="output_zarr" format="zarr" label="${tool.name} on ${on_string}: Zarr output"/>
+    </outputs>
+    <tests>
+        <test expect_num_outputs="1">
+            <param name="input_image" location="https://zenodo.org/records/20029977/files/visium-breast-cancer-label.tif"/>
+            <param name="stem" value="visium-breast-cancer"/>
+            <param name="image_type" value="label"/>
+            <output name="output_zarr">
+                <extra_files type="file" name="visium-breast-cancer-label.zarr/OME/METADATA.ome.xml">
+                    <assert_contents>
+                        <has_text text="&lt;Description&gt;{&quot;shape&quot;: [21571, 19505]}&lt;/Description&gt;&lt;Pixels BigEndian=&quot;true&quot; DimensionOrder=&quot;XYZCT&quot;"/>
+                    </assert_contents>
+                </extra_files>
+            </output>
+        </test>
+        <test expect_num_outputs="1">
+            <param name="input_image" location="https://zenodo.org/records/20029977/files/tissue_image.tif"/>
+            <param name="stem" value="visium-breast-cancer"/>
+            <param name="image_type" value="raw"/>
+            <output name="output_zarr">
+                <extra_files type="file" name="visium-breast-cancer-raw.zarr/OME/METADATA.ome.xml">
+                    <assert_contents>
+                        <has_text_matching expression="Pixels BigEndian=&quot;true&quot; DimensionOrder=&quot;XYZCT&quot; ID=&quot;Pixels:0&quot; Interleaved=&quot;false&quot; PhysicalSizeX=&quot;0.5475[0-9]+&quot; PhysicalSizeXUnit=&quot;µm&quot; PhysicalSizeY=&quot;0.5476[0-9]+&quot; PhysicalSizeYUnit=&quot;µm&quot; SignificantBits=&quot;8&quot; SizeC=&quot;3&quot; SizeT=&quot;1&quot; SizeX=&quot;19505&quot; SizeY=&quot;21571&quot; SizeZ=&quot;1&quot; Type=&quot;uint8&quot;"/>
+                    </assert_contents>
+                </extra_files>
+            </output>
+        </test>
+    </tests>
+    <help><![CDATA[
+This tool converts image data into the Zarr format and consolidates its metadata to improve performance in downstream visualization.
+
+It typically processes label images generated by **WebAtlas Generate Image** and raw images provided as input or generated within the WebAtlas workflow.
+
+----
+
+**Supported Input Types**
+
+- **TIFF image** (including JPEG-compressed TIFF)
+- **JPEG image**
+
+----
+
+**Processing Steps**
+
+- (If applicable) Decompression of JPEG-compressed TIFF images prior to conversion 
+- Conversion of the input image to Zarr format using *bioformats2raw*
+- Consolidation of Zarr metadata
+
+----
+
+**Metadata Consolidation**
+
+Zarr datasets normally store metadata in many small files. This tool consolidates them into a single metadata file.
+
+This can significantly reduce the time necessary to load the metadata in downstream visualization.
+
+----
+
+**Output**
+
+- **Zarr dataset (image with consolidated metadata)**
+
+The output is used as input for the downstream WebAtlas tools **WebAtlas OME Zarr Metadata**, **WebAtlas Build Vitessce Config**, and **WebAtlas Write**.
+    ]]></help>
+    <expand macro="citations"/>
+</tool>
\ No newline at end of file
diff --git a/tools/webatlas/generate_image.xml b/tools/webatlas/generate_image.xml
new file mode 100644
index 0000000000..0fb625dbb3
--- /dev/null
+++ b/tools/webatlas/generate_image.xml
@@ -0,0 +1,317 @@
+<tool id="webatlas_generate_image" name="WebAtlas Generate Image" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" python_template_version="3.5" profile="@PROFILE_VERSION@">
+    <description>Generate label/raw TIFF image from spatial metadata</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements"/>
+    <command detect_errors="exit_code"><![CDATA[
+    #if $img_type.img_type_selector == "label":
+        #if $img_type.input_type.input_type_selector == "visium":
+            #if $img_type.input_type.file_type_visium.file_type_selector_visium == "zip":
+                mkdir unpacked_spaceranger &&
+                unzip '$input_visium_zip' -d unpacked_spaceranger &&
+                generate_image.py --stem '$stem' --img_type label --file_type visium --file_path unpacked_spaceranger
+                @VISIUM_LABEL_COMMAND@
+                mv '$stem'-label.tif '$output_img'
+            #else if $img_type.input_type.file_type_visium.file_type_selector_visium == "h5ad":
+                ln -s '$input_visium_h5ad' input.h5ad &&
+                generate_image.py --stem '$stem' --img_type label --file_type visium --file_path input.h5ad
+                @VISIUM_LABEL_COMMAND@
+                mv '$stem'-label.tif '$output_img'
+            #end if
+        #else if $img_type.input_type.input_type_selector == "xenium":
+            mkdir unpacked_xenium &&
+            unzip '$input_xenium' -d unpacked_xenium &&
+            generate_image.py --stem '$stem' --img_type label --file_type xenium --file_path unpacked_xenium
+            --ref_img '$ref_img'
+            --args "{
+            #if $resolution:
+                'resolution': $resolution
+            #end if
+            }"
+            &&
+            mv '$stem'-label.tif '$output_img'
+        #else if $img_type.input_type.input_type_selector == "merscope":
+            mkdir unpacked_merscope &&
+            unzip '$input_merscope_label' -d unpacked_merscope &&
+            generate_image.py --stem '$stem' --img_type label --file_type merscope --file_path unpacked_merscope
+            --ref_img '$ref_img'
+            @Z_INDEX_COMMAND@
+            mv '$stem'-label.tif '$output_img'
+        #end if
+    #else if $img_type.img_type_selector == "raw":
+        mkdir unpacked_merscope &&
+        unzip '$input_merscope_raw' -d unpacked_merscope &&
+        generate_image.py --stem '$stem' --img_type raw --file_type merscope --file_path unpacked_merscope
+        @Z_INDEX_COMMAND@
+        mv '$stem'-raw.tif '$output_img'
+    #end if
+    ]]></command>
+    <inputs>
+        <conditional name="img_type">
+            <param name="img_type_selector" type="select" label="Image type to generate">
+                <option value="label">Label image</option>
+                <option value="raw">Raw image</option>
+            </param>
+            <when value="label">
+                <conditional name="input_type">
+                    <param name="input_type_selector" type="select" label="Choose the type of input data" help="Choose the format of the input dataset to generate a label image from.">
+                        <option value="visium">Visium data (SpaceRanger output or H5AD AnnData file)</option>
+                        <option value="xenium">Xenium output archive (ZIP)</option>
+                        <option value="merscope">MERSCOPE output archive (ZIP)</option>
+                    </param>
+                    <when value="visium">
+                        <conditional name="file_type_visium">
+                            <param name="file_type_selector_visium" type="select" label="Choose the type of input file">
+                                <option value="zip">SpaceRanger output archive (ZIP)</option>
+                                <option value="h5ad">Input AnnData file (H5AD)</option>
+                            </param>
+                            <when value="h5ad">
+                                <param name="input_visium_h5ad" type="data" format="h5ad" label="Input AnnData file (H5AD)"/>
+                            </when>
+                            <when value="zip">
+                                <param name="input_visium_zip" type="data" format="zip" label="SpaceRanger output archive (ZIP)"/>
+                            </when>
+                        </conditional>
+                        <param name="ref_img_visium" argument="--ref_img" type="data" format="tiff" optional="true" label="Reference image" help="Reference image from which to get the shape for the label image. If left empty the shape will be derived from the AnnData."/>
+                        <expand macro="stem"/>
+                        <section name="sec_advanced_options" title="Advanced options" expanded="false">
+                            <expand macro="obs_subset"/>
+                            <param argument="--sample_id" type="text" optional="true" label="Sample ID" help="Specify a sample ID if the dataset contains multiple samples and you wish to visualize a specific one.">
+                                <expand macro="sanitizer_options"/>
+                            </param>
+                            <param argument="--relative_size" type="text" optional="true" label="Relative size" help="Optional numerical 'obs' column name that holds a multiplier for the spot diameter. Only useful for data that has been processed to merge spots.">
+                                <expand macro="sanitizer_options"/>
+                            </param>
+                        </section>
+                    </when>
+                    <when value="xenium">
+                        <param name="input_xenium" type="data" format="zip" label="Xenium output archive (ZIP)"/>
+                        <expand macro="ref_img"/>
+                        <expand macro="stem"/>
+                        <param name="resolution" type="float" value="0.2125" optional="true" label="Pixel resolution" help="Pixel resolution used to convert Xenium spatial coordinates. Default value: 0.2125"/>
+                    </when>
+                    <when value="merscope">
+                        <param name="input_merscope_label" type="data" format="zip" label="MERSCOPE output archive (ZIP)"/>
+                        <expand macro="ref_img"/>
+                        <expand macro="stem"/>
+                        <expand macro="z_index"/>
+                    </when>
+                </conditional>
+            </when>
+            <when value="raw">
+                <param name="input_merscope_raw" type="data" format="zip" label="MERSCOPE output archive (ZIP)"/>
+                <expand macro="stem"/>
+                <expand macro="z_index"/>
+            </when>
+        </conditional>
+    </inputs>
+    <outputs>
+        <data name="output_img" format="tiff" label="${tool.name} on ${on_string}: $img_type_selector TIFF image"/>
+    </outputs>
+    <tests>
+    <test expect_num_outputs="1">
+        <conditional name="img_type">
+            <param name="img_type_selector" value="label"/>
+            <conditional name="input_type">
+                <param name="input_type_selector" value="visium"/>
+                <conditional name="file_type_visium">
+                    <param name="file_type_selector_visium" value="h5ad"/>
+                    <param name="input_visium_h5ad" location="https://zenodo.org/records/20029977/files/input.h5ad"/>
+                </conditional>
+                <param name="stem" value="visium_h5ad"/>
+            </conditional>
+        </conditional>
+        <output name="output_img">
+            <assert_contents>
+                <has_size value="841661656" delta="100"/>
+            </assert_contents>
+        </output>
+    </test>
+
+    <test expect_num_outputs="1">
+        <conditional name="img_type">
+            <param name="img_type_selector" value="label"/>
+            <conditional name="input_type">
+                <param name="input_type_selector" value="visium"/>
+                <conditional name="file_type_visium">
+                    <param name="file_type_selector_visium" value="h5ad"/>
+                    <param name="input_visium_h5ad" location="https://zenodo.org/records/20029977/files/input.h5ad"/>
+                </conditional>
+                <param name="stem" value="visium_h5ad"/>
+                <section name="sec_advanced_options">
+                    <conditional name="obs_subset_conditional">
+                        <param name="obs_subset" value="true"/>
+                        <param name="obs_subset_column" value="in_tissue"/>
+                        <param name="obs_subset_values" value="1"/>
+                    </conditional>
+                </section>
+            </conditional>
+        </conditional>
+        <output name="output_img">
+            <assert_contents>
+                <has_size value="841661656" delta="100"/>
+            </assert_contents>
+        </output>
+    </test>
+
+    <test expect_num_outputs="1">
+        <conditional name="img_type">
+            <param name="img_type_selector" value="label"/>
+            <conditional name="input_type">
+                <param name="input_type_selector" value="visium"/>
+                <conditional name="file_type_visium">
+                    <param name="file_type_selector_visium" value="h5ad"/>
+                    <param name="input_visium_h5ad" location="https://zenodo.org/records/20029977/files/input.h5ad"/>
+                </conditional>
+                <param name="stem" value="visium_h5ad"/>
+                <section name="sec_advanced_options">
+                    <conditional name="obs_subset_conditional">
+                        <param name="obs_subset" value="true"/>
+                        <param name="obs_subset_column" value="in_tissue"/>
+                        <param name="obs_subset_values" value="0"/>
+                    </conditional>
+                </section>
+            </conditional>
+        </conditional>
+        <output name="output_img">
+            <assert_contents>
+                <has_size value="841661672" delta="100"/>
+            </assert_contents>
+        </output>
+    </test>
+    
+    <test expect_num_outputs="1">
+        <conditional name="img_type">
+            <param name="img_type_selector" value="label"/>
+            <conditional name="input_type">
+                <param name="input_type_selector" value="visium"/>
+                <conditional name="file_type_visium">
+                    <param name="file_type_selector_visium" value="zip"/>
+                    <param name="input_visium_zip" location="https://zenodo.org/records/20029977/files/spaceranger.zip"/>
+                </conditional>
+                <param name="stem" value="visium-breast-cancer"/>
+            </conditional>
+        </conditional>
+        <output name="output_img">
+            <assert_contents>
+                <has_size value="841661656" delta="100"/>
+            </assert_contents>
+        </output>
+    </test>
+
+    <test expect_num_outputs="1">
+        <conditional name="img_type">
+            <param name="img_type_selector" value="label"/>
+            <conditional name="input_type">
+                <param name="input_type_selector" value="xenium"/>
+                <param name="input_xenium" location="https://zenodo.org/records/20029977/files/Xenium_Prime_MultiCellSeg_Mouse_Ileum_tiny_outs.zip"/>
+                <param name="ref_img" location="https://zenodo.org/records/20029977/files/morphology_tiny.ome.tif"/>
+                <param name="stem" value="xenium-tiny"/>
+            </conditional>
+        </conditional>
+        <output name="output_img">
+            <assert_contents>
+                <has_size value="20389114" delta="1000"/>
+            </assert_contents>
+        </output>
+    </test>
+    
+    <test expect_num_outputs="1">
+        <conditional name="img_type">
+            <param name="img_type_selector" value="label"/>
+            <conditional name="input_type">
+                <param name="input_type_selector" value="merscope"/>
+                <param name="input_merscope_label" location="https://zenodo.org/records/20029977/files/merscope.zip"/>
+                <param name="ref_img" location="https://zenodo.org/records/20029977/files/shape.tiff"/>
+                <param name="stem" value="merscope-label"/>
+            </conditional>
+        </conditional>
+        <output name="output_img">
+            <assert_contents>
+                <has_size value="14838160" delta="100"/>
+            </assert_contents>
+        </output>
+    </test>
+    
+    <test expect_num_outputs="1">
+        <conditional name="img_type">
+            <param name="img_type_selector" value="raw"/>
+            <param name="input_merscope_raw" location="https://zenodo.org/records/20029977/files/merscope.zip"/>
+            <param name="stem" value="merscope-raw"/>
+        </conditional>
+        <output name="output_img">
+            <assert_contents>
+                <has_size value="62618255" delta="1000"/>
+            </assert_contents>
+        </output>
+    </test>
+    </tests>
+    <help><![CDATA[
+This tool generates a label TIFF image based on spatial metadata of the input data.
+
+For MERSCOPE data, it can additionally concatenate raw images into a single multichannel TIFF image.
+
+----
+
+**Supported Input Types**
+
+- **Visium AnnData (H5AD)**
+- **Visium SpaceRanger output archive (ZIP)**
+- **Xenium output archive (ZIP)**
+- **MERSCOPE output archive (ZIP)**
+
+----
+
+**Functionality**
+
+Depending on the input type, label images are generated as follows:
+
+- **Visium**
+    If SpaceRanger is provided as input, it is first converted into an AnnData object.
+    The observations are then reindexed to ensure numerical values, which are required for label image generation.
+    A label image TIFF file is then generated, with spots based on the spatial coordinates of the AnnData object.
+    Each spot is assigned a unique identifier, for example, a cell ID.
+
+- **Xenium**
+    A label image is generated with labels based on cell segmentation polygons from the Xenium output.
+    These polygons are converted into pixel coordinates and applied to the output image, assigning a unique label (e.g. cell ID) to each cell.
+
+- **MERSCOPE**
+    A label image is generated based on boundary information stored in the MERSCOPE data. Optionally, multiple Z-indices of the MERSCOPE data can be processed.
+
+Additionally, this tool can concatenate raw TIFF images from MERSCOPE into a single multichannel TIFF image per Z-index.
+This process is performed independently of the label image generation.
+
+----
+
+**Reference Image**
+    A reference image is required to determine the dimensions of the output label image.
+    For Visium data, this is optional, as the shape can be derived from the AnnData.
+
+----
+
+**Input type specific parameters**
+
+- **Visium**
+    - Subset AnnData on an obs column: Allows filtering of observations based on a specified column in the *obs* table. Only observations matching the specified values are kept in the dataset.
+    - Sample ID: Specify a sample ID if the dataset contains multiple samples and you wish to visualize a specific one.
+    - Relative size: Optional numerical *obs* column name that holds a multiplier for the spot diameter. Only useful for data that has been processed to merge spots.
+
+- **Xenium**
+    - Pixel resolution: Pixel resolution used for converting Xenium spatial coordinates to pixel coordinates.
+
+- **MERSCOPE**
+    - Z index: Z index of the MERSCOPE data that should be processed.
+
+----
+
+**Output**
+
+- **Label image (TIFF)**
+- **Multichannel raw image (TIFF, MERSCOPE only)**
+
+The output is used as input for the downstream WebAtlas tools **WebAtlas Consolidate Metadata** and **WebAtlas Write**.
+    ]]></help>
+    <expand macro="citations"/>
+</tool>
\ No newline at end of file
diff --git a/tools/webatlas/macros.xml b/tools/webatlas/macros.xml
new file mode 100644
index 0000000000..edc145341c
--- /dev/null
+++ b/tools/webatlas/macros.xml
@@ -0,0 +1,189 @@
+<macros>
+    <token name="@TOOL_VERSION@">0.5.3</token>
+    <token name="@VERSION_SUFFIX@">0</token>
+    <token name="@PROFILE_VERSION@">25.1</token>
+    <xml name="requirements">
+        <requirements>
+            <container type="docker">quay.io/bgruening/galaxy-webatlas:v0.5.3-1</container>
+        </requirements>
+    </xml>
+
+    <!-- router -->
+    <token name="@H5AD_TO_ZARR_COMMAND_BLOCK@"><![CDATA[
+        --chunk_size $chunk_size
+        #if $compute_embeddings:
+            --compute_embeddings
+        #end if
+        #if $var_index:
+            --var_index '$var_index'
+        #end if
+        #if $obs_subset_conditional.obs_subset == 'true':
+            --obs_subset "['$obs_subset_column', ${obs_subset_values.replace(' ', '').split(',')}]"
+        #end if
+        #if $var_subset_conditional.var_subset == 'true':
+            --var_subset "['$var_subset_column', ${var_subset_values.replace(' ', '').split(',')}]"
+        #end if
+        #if $batch_processing_conditional.batch_processing == 'true':
+            --batch_processing
+            --batch_size $batch_size
+        #end if
+        #if not $consolidate_metadata:
+            --consolidate_metadata=False
+        #end if
+        &&
+        ]]>
+    </token>
+    <xml name="stem">
+        <param name="stem" type="text" optional="false" label="Prefix for the output file(s)" help="Prefix used for the output file names. E.g. 'visium-breast-cancer'. Use the same prefix across WebAtlas tools for the same project and dataset, to ensure compatibility.">
+            <expand macro="sanitizer_prefix"/>
+        </param>
+    </xml>
+    <xml name="save_h5ad">
+        <param argument="--save_h5ad" type="boolean" checked="false" label="Save H5AD file" help="Save the processed AnnData object as an H5AD file in addition to the Zarr output."/>
+    </xml>
+    <xml name="h5ad_to_zarr_parameters">
+        <param argument="--chunk_size" type="integer" min="1" value="10" label="Output Zarr column chunk size." help="Default value: 10"/>
+        <param argument="--compute_embeddings" type="boolean" checked="false" optional="true" label="Compute embeddings" help="Compute 'X_umap' and 'X_pca' embeddings if they are not already present in the input data."/>
+        <section name="sec_advanced_options" title="Advanced options" expanded="false">
+            <param argument="--var_index" type="text" optional="true" label="Alternative var index" help="Alternative 'var' column name with 'var' names to be used in the visualization.">
+                <expand macro="sanitizer_options"/>
+            </param>
+            <conditional name="obs_subset_conditional">
+                <param name="obs_subset" type="select" label="Subset AnnData on an obs column" help="Subset the AnnData object on a specific observation (obs) column with one or more values.">
+                    <option value="false">No</option>
+                    <option value="true">Yes</option>
+                </param>
+                <when value="true">
+                    <param name="obs_subset_column" type="text" optional="false" label="Observation column name" help="Observation column to apply the subset on.">
+                        <expand macro="sanitizer_options"/>
+                    </param>
+                    <param name="obs_subset_values" type="text" optional="false" label="Values to keep" help="Comma-separated list of values to keep.">
+                        <expand macro="sanitizer_option_values"/>
+                    </param>
+                </when>
+                <when value="false">
+                </when>
+            </conditional>
+            <conditional name="var_subset_conditional">
+                <param name="var_subset" type="select" label="Subset AnnData on a var column" help="Subset the AnnData object on a specific variable (var) column with one or more values.">
+                    <option value="false">No</option>
+                    <option value="true">Yes</option>
+                </param>
+                <when value="true">
+                    <param name="var_subset_column" type="text" optional="false" label="Variable column name" help="Variable column to apply the subset on. E.g. 'gene_ids'.">
+                        <expand macro="sanitizer_options"/>
+                    </param>
+                    <param name="var_subset_values" type="text" optional="false" label="Values to keep" help="Comma-separated list of values to keep. E.g. 'A1CF,MSN'.">
+                        <expand macro="sanitizer_option_values"/>
+                    </param>
+                </when>
+                <when value="false">
+                </when>
+            </conditional>
+            <conditional name="batch_processing_conditional">
+                <param name="batch_processing" type="select" label="Enable batch processing" help="Write the expression matrix to Zarr incrementally instead of loading the full matrix into memory. Useful for large datasets.">
+                    <option value="false">No</option>
+                    <option value="true">Yes</option>
+                </param>
+                <when value="true">
+                    <param argument="--batch_size" type="integer" min="1" value="10000" label="Batch size" help="The amount of rows (if matrix is in CSR format) or columns (if matrix is dense or in CSC format) of the expression matrix to process at a time when batch processing. Default value: 10000."/>
+                </when>
+                <when value="false">
+                </when>
+            </conditional>
+            <param argument="--consolidate_metadata" type="boolean" checked="true" optional="true" label="Consolidate metadata" help="Whether to consolidate output zarr metadata. Keep this enabled unless you need unconsolidated metadata for a specific use."/>
+        </section>
+    </xml>
+
+    <!-- generate_image -->
+    <token name="@VISIUM_LABEL_COMMAND@"><![CDATA[
+        #if $ref_img_visium:
+            --ref_img '$ref_img_visium'
+        #end if
+        --args "{
+        #if $obs_subset_conditional.obs_subset == 'true':
+            'obs_subset': ['$obs_subset_column', ${obs_subset_values.replace(' ', '').split(',')}],
+        #end if
+        #if $sample_id:
+            'sample_id': '$sample_id',
+        #end if
+        #if $relative_size:
+            'relative_size': '$relative_size',
+        #end if
+        }"
+        &&
+        ]]>
+    </token>
+    <token name="@Z_INDEX_COMMAND@"><![CDATA[
+        --args "{
+            'z_index': $z_index
+        }"
+        &&
+        ]]>
+    </token>
+    <xml name="ref_img">
+        <param argument="--ref_img" type="data" format="tiff,tif" optional="false" label="Reference image" help="Reference image used to determine the dimensions of the output image."/>
+    </xml>
+    <xml name="obs_subset">
+        <conditional name="obs_subset_conditional">
+            <param name="obs_subset" type="select" label="Subset AnnData on an obs column" help="Subset the AnnData object on a specific observation (obs) column with one or more values.">
+                <option value="false">No</option>
+                <option value="true">Yes</option>
+            </param>
+            <when value="true">
+                <param name="obs_subset_column" type="text" optional="false" label="Observation column name" help="Observation column to apply the subset on.">
+                    <expand macro="sanitizer_options"/>
+                </param>
+                <param name="obs_subset_values" type="text" optional="false" label="Values to keep" help="Comma-separated list of values to keep.">
+                    <expand macro="sanitizer_option_values"/>
+                </param>
+            </when>
+            <when value="false">
+            </when>
+        </conditional>
+    </xml>
+    <xml name="z_index">
+        <param name="z_index" type="integer" optional="true" value="0" label="Z index" help="Z index to process. Run the tool again to generate additional Z planes. Default value: 0."/>
+    </xml>
+
+    <!-- sanitizers -->
+    <xml name="sanitizer_prefix">
+        <sanitizer invalid_char="">
+            <valid initial="string.ascii_letters,string.digits">
+                <add value="_"/>
+                <add value="-"/>
+            </valid>
+        </sanitizer>
+    </xml>
+    <xml name="sanitizer_options">
+        <sanitizer invalid_char="">
+            <valid initial="string.ascii_letters,string.digits">
+                <add value="_"/>
+                <add value="-"/>
+                <add value="."/>
+            </valid>
+        </sanitizer>
+    </xml>
+    <xml name="sanitizer_option_values">
+        <sanitizer invalid_char="">
+            <valid initial="string.ascii_letters,string.digits">
+                <add value="_"/>
+                <add value="-"/>
+                <add value="."/>
+                <add value=","/>
+            </valid>
+        </sanitizer>
+    </xml>
+    <xml name="sanitizer_printable">
+        <sanitizer invalid_char="">
+            <valid initial="string.printable"/>
+        </sanitizer>
+    </xml>
+    <xml name="citations">
+        <citations>
+            <citation type="doi">
+                https://doi.org/10.1038/s41592-024-02371-x
+            </citation>
+        </citations>
+    </xml>
+</macros>
diff --git a/tools/webatlas/ome_zarr_metadata.xml b/tools/webatlas/ome_zarr_metadata.xml
new file mode 100644
index 0000000000..e97e86916b
--- /dev/null
+++ b/tools/webatlas/ome_zarr_metadata.xml
@@ -0,0 +1,79 @@
+<tool id="webatlas_ome_zarr_metadata" name="WebAtlas OME Zarr Metadata" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE_VERSION@">
+    <description>extraction as JSON</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements"/>
+    <command detect_errors="exit_code"><![CDATA[
+        ome_zarr_metadata.py --xml_path '$input_zarr.extra_files_path/$input_zarr.metadata.store_root/OME/METADATA.ome.xml' > output.json
+    ]]></command>
+    <inputs>
+        <param name="input_zarr" type="data" format="zarr,ome_zarr" label="Zarr directory"/>
+    </inputs>
+    <outputs>
+        <data name="output_json" format="json" label="${tool.name} on ${on_string}" from_work_dir="output.json"/>
+    </outputs>
+    <tests>
+    <test expect_num_outputs="1">
+        <param name="input_zarr" location="https://zenodo.org/records/20029977/files/visium-breast-cancer-label.zarr.zip"/>
+        <output name="output_json">
+            <assert_contents>
+                <has_json_property_with_text property="dimOrder" text="XYZCT"/>
+                <has_json_property_with_text property="X" text="19505"/>
+                <has_json_property_with_text property="Y" text="21571"/>
+                <has_json_property_with_text property="Z" text="1"/>
+                <has_json_property_with_text property="C" text="1"/>
+                <has_json_property_with_text property="T" text="1"/>
+                <has_size value="101" delta="5"/>
+            </assert_contents>
+        </output>
+    </test>
+    <test expect_num_outputs="1">
+        <param name="input_zarr" location="https://zenodo.org/records/20029977/files/visium-breast-cancer-raw.zarr.zip"/>
+        <output name="output_json">
+            <assert_contents>
+                <has_json_property_with_text property="dimOrder" text="XYZCT"/>
+                <has_json_property_with_text property="X" text="19505"/>
+                <has_json_property_with_text property="Y" text="21571"/>
+                <has_json_property_with_text property="Z" text="1"/>
+                <has_json_property_with_text property="C" text="3"/>
+                <has_json_property_with_text property="T" text="1"/>
+                <has_size value="101" delta="5"/>
+            </assert_contents>
+        </output>
+    </test>
+    </tests>
+    <help><![CDATA[
+This tool extracts image metadata from a Zarr dataset containing OME metadata.
+
+It is typically used on the output of **WebAtlas Consolidate Metadata** and provides metadata required for downstream visualization configuration.
+
+----
+
+**Input**
+
+- **Zarr dataset (image)**
+  generated by **WebAtlas Consolidate Metadata**
+
+----
+
+**Functionality**
+
+The tool reads the OME XML metadata file stored within the Zarr dataset and extracts basic image metadata.
+
+The extracted metadata includes:
+
+- Dimension order (e.g. XYZCT)
+- Image dimensions (X, Y, Z, C, T)
+- Channel names
+
+----
+
+**Output**
+
+- **Metadata (JSON)**
+
+The output is used as input for the downstream WebAtlas tool **WebAtlas Build Vitessce Config**.
+    ]]></help>
+    <expand macro="citations"/>
+</tool>
\ No newline at end of file
diff --git a/tools/webatlas/router.xml b/tools/webatlas/router.xml
new file mode 100644
index 0000000000..89a5204e84
--- /dev/null
+++ b/tools/webatlas/router.xml
@@ -0,0 +1,421 @@
+<tool id="webatlas_router" name="WebAtlas Process Spatial datasets" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" python_template_version="3.5" profile="@PROFILE_VERSION@">
+    <description>into AnnData-Zarr</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements"/>
+    <command detect_errors="exit_code"><![CDATA[
+        #if $input_type.input_type_selector == 'h5ad':
+            ln -s '$input_h5ad' input.h5ad &&
+            process_h5ad.py --path input.h5ad --stem '$stem'
+            @H5AD_TO_ZARR_COMMAND_BLOCK@
+            mkdir -p '$output_zarr.extra_files_path' &&
+            mv '$stem'-anndata.zarr '$output_zarr.extra_files_path'
+        #else if $input_type.input_type_selector == 'spaceranger':
+            mkdir unpacked_spaceranger &&
+            unzip '$input_spaceranger' -d unpacked_spaceranger &&
+            process_spaceranger.py --path unpacked_spaceranger --stem '$stem'
+            #if not $load_clusters:
+                --load_clusters=False
+            #end if
+            #if not $load_embeddings:
+                --load_embeddings=False
+            #end if
+            #if $load_raw:
+                --load_raw
+            #end if
+            #if $save_h5ad:
+                --save_h5ad
+            #end if
+            @H5AD_TO_ZARR_COMMAND_BLOCK@
+            #if $save_h5ad:
+                mv 'tmp-${stem}.h5ad' '$output_h5ad' &&
+            #end if
+            mkdir -p '$output_zarr.extra_files_path' &&
+            mv '$stem'-anndata.zarr '$output_zarr.extra_files_path'
+        #else if $input_type.input_type_selector == 'xenium':
+            mkdir unpacked_xenium &&
+            unzip '$input_xenium' -d unpacked_xenium &&
+            process_xenium.py --path unpacked_xenium --stem '$stem'
+            #if not $spatial_as_pixel:
+                --spatial_as_pixel=False
+            #end if
+            #if $resolution:
+                --resolution $resolution
+            #end if
+            #if $save_h5ad:
+                --save_h5ad
+            #end if
+            @H5AD_TO_ZARR_COMMAND_BLOCK@
+            #if $save_h5ad:
+                mv 'tmp-${stem}.h5ad' '$output_h5ad' &&
+            #end if
+            mkdir -p '$output_zarr.extra_files_path' &&
+            mv '$stem'-anndata.zarr '$output_zarr.extra_files_path'
+        #else if $input_type.input_type_selector == 'merscope':
+            mkdir unpacked_merscope &&
+            unzip '$input_merscope' -d unpacked_merscope &&
+            process_merscope.py --path unpacked_merscope --stem '$stem' --filter_prefix '$filter_prefix'
+            #if $save_h5ad:
+                --save_h5ad
+            #end if
+            @H5AD_TO_ZARR_COMMAND_BLOCK@
+            #if $save_h5ad:
+                mv 'tmp-${stem}.h5ad' '$output_h5ad' &&
+            #end if
+            mkdir -p '$output_zarr.extra_files_path' &&
+            mv '$stem'-anndata.zarr '$output_zarr.extra_files_path'
+        ## #else if $input_type.input_type_selector == 'molecules':
+        ##     process_molecules.py --path $input_molecules --stem $stem --has_header $has_header --gene_col_name $gene_col_name --x_col_name $x_col_name --y_col_name $y_col_name --delimiter $delimiter --x_scale $x_scale --y_scale $y_scale --x_offset $x_offset --y_offset $y_offset --gene_col_idx $gene_col_idx --x_col_idx $x_col_idx --y_col_idx $y_col_idx --filter_col_name $filter_col_name --filter_col_idx $filter_col_idx --filter_col_value $filter_col_value &&
+        ##     mv '$stem'*.json $output_json
+        #end if
+    ]]></command>
+    <inputs>
+        <conditional name="input_type">
+            <param name="input_type_selector" type="select" label="Choose the type of input data" help="Choose the format of the input dataset to process into AnnData-Zarr.">
+                <option value="h5ad">Input AnnData file (H5AD)</option>
+                <option value="spaceranger">SpaceRanger output archive (ZIP)</option>
+                <option value="xenium">Xenium output archive (ZIP)</option>
+                <option value="merscope">MERSCOPE output archive (ZIP)</option>
+                <!-- Currently there is no usecase for this option. It can be implemented on request -->
+                <!-- <option value="molecules">Molecules data in csv/tsv file</option> -->
+            </param>
+            <when value="h5ad">
+                <param name="input_h5ad" type="data" format="h5ad" label="Input AnnData file (H5AD)"/>
+                <expand macro="stem"/>
+                <expand macro="h5ad_to_zarr_parameters"/>
+            </when>
+            <when value="spaceranger">
+                <param name="input_spaceranger" type="data" format="zip" label="SpaceRanger output archive (ZIP)"/>
+                <expand macro="stem"/>
+                <param argument="--load_clusters" type="boolean" checked="true" optional="true" label="Include cluster files" help="If cluster files should be included in the AnnData object."/>
+                <param argument="--load_embeddings" type="boolean" checked="true" optional="true" label="Include embeddings" help="If embedding coordinates files should be included in the AnnData object."/>
+                <param argument="--load_raw" type="boolean" checked="false" optional="true" label="Use raw matrix count file" help="If the raw matrix count file should be loaded instead of the filtered matrix."/>
+                <expand macro="h5ad_to_zarr_parameters"/>
+                <expand macro="save_h5ad"/>
+            </when>
+            <when value="xenium">
+                <param name="input_xenium" type="data" format="zip" label="Xenium output archive (ZIP)"/>
+                <expand macro="stem"/>
+                <param argument="--spatial_as_pixel" type="boolean" checked="true" label="Convert spatial coordinates to pixel coordinates" help="Convert Xenium spatial coordinates to pixel coordinates using the specified resolution."/>
+                <param argument="--resolution" type="float" value="0.2125" optional="true" label="Pixel resolution" help="Pixel resolution to use for converting spatial coordinates to pixel coordinates. Default value: 0.2125"/>
+                <expand macro="h5ad_to_zarr_parameters"/>
+                <expand macro="save_h5ad"/>
+            </when>
+            <when value="merscope">
+                <param name="input_merscope" type="data" format="zip" label="MERSCOPE output archive (ZIP)"/>
+                <expand macro="stem"/>
+                <param argument="--filter_prefix" type="text" value="Blank-" optional="true" label="Filter prefix" help="Prefix to filter out of the data. Default value: 'Blank-'.">
+                    <expand macro="sanitizer_options"/>
+                </param>
+                <expand macro="h5ad_to_zarr_parameters"/>
+                <expand macro="save_h5ad"/>
+            </when>
+            <!-- <when value="molecules">
+                <param name="input_molecules" type="data" format="csv,tsv" label="Molecules file"/>
+                <expand macro="stem"/>
+                <param name="has_header" type="boolean" checked="true" optional="true" label="Does the input file contain a header row?"/>
+                <param name="gene_col_name" type="text" value="Name" optional="true" label="Column header name where gene names are stored." help="Default value: Name"/>
+                <param name="x_col_name" type="text" value="x_int" optional="true" label="Column header name where 'X' coordinates are stored." help="Default value: x_int"/>
+                <param name="y_col_name" type="text" value="y_int" optional="true" label="Column header name where 'Y' coordinates are stored." help="Default value: y_int"/>
+                <param name="delimiter" type="text" value="\t" optional="true" label="Input file delimiter." help="Default value: \t"/>
+                <param name="x_scale" type="float" value="1.0" optional="true" label="Scale to multiply 'X' coordinates by." help="Default value: 1.0"/>
+                <param name="y_scale" type="float" value="1.0" optional="true" label="Scale to multiply 'Y' coordinates by." help="Default value: 1.0"/>
+                <param name="x_offset" type="float" value="0.0" optional="true" label="Offset to add to 'X' coordinates." help="Default value: 0.0"/>
+                <param name="y_offset" type="float" value="0.0" optional="true" label="Offset to add to 'Y' coordinates." help="Default value: 0.0"/>
+                <param name="gene_col_idx" type="integer" optional="true" label="Column index where gene names are stored if header is not present."/>
+                <param name="x_col_idx" type="integer" optional="true" label="Column index where 'X' coordinates are stored if header is not present."/>
+                <param name="y_col_idx" type="integer" optional="true" label="Column index where 'Y' coordinates are stored if header is not present." />
+                <param name="filter_col_name" type="text" optional="true" label="Column header name storing values to filter data."/>
+                <param name="filter_col_idx" type="integer" optional="true" label="Column index storing values to filter data if header is not present."/>
+                <param name="filter_col_value" type="text" optional="true" label="Value expected in filter column. If a row has a different value it will not be written to the output file."/>
+            </when> -->
+        </conditional>
+    </inputs>
+    <outputs>
+        <data name="output_h5ad" format="h5ad" label="${tool.name} on ${on_string}: H5AD output">
+            <filter>'h5ad' not in input_type['input_type_selector'] and input_type['save_h5ad']
+            </filter>
+        </data>
+        <data name="output_zarr" format="zarr" label="${tool.name} on ${on_string}: Zarr output"/>
+        <!-- <data name="output_json" format="json" label="${tool.name} on ${on_string}">
+            <filter>input_type['input_type_selector'] == 'molecules'</filter>
+        </data> -->
+    </outputs>
+    <tests>
+    <test expect_num_outputs="1">
+        <conditional name="input_type">
+            <param name="input_type_selector" value="h5ad"/>
+            <param name="input_h5ad" location="https://zenodo.org/records/20029977/files/input.h5ad"/>
+            <param name="stem" value="h5ad"/>
+        </conditional>
+        <output name="output_zarr">
+            <extra_files type="file" name="h5ad-anndata.zarr/.zmetadata">
+                <assert_contents>
+                    <has_text text="&quot;zarr_format&quot;: 2"/>
+                    <has_text text="feature_types"/>
+                </assert_contents>
+            </extra_files>
+        </output>
+    </test>
+
+    <test expect_num_outputs="1">
+        <conditional name="input_type">
+            <param name="input_type_selector" value="h5ad"/>
+            <param name="input_h5ad" location="https://zenodo.org/records/20029977/files/input.h5ad"/>
+            <param name="stem" value="h5ad"/>
+            <section name="sec_advanced_options">
+                <conditional name="obs_subset_conditional">
+                    <param name="obs_subset" value="true"/>
+                    <param name="obs_subset_column" value="in_tissue"/>
+                    <param name="obs_subset_values" value="1"/>
+                </conditional>
+            </section>
+        </conditional>
+        <output name="output_zarr">
+            <extra_files type="file" name="h5ad-anndata.zarr/.zmetadata">
+                <assert_contents>
+                    <has_text text="&quot;zarr_format&quot;: 2"/>
+                    <has_text text="feature_types"/>
+                </assert_contents>
+            </extra_files>
+        </output>
+    </test>
+
+    <test expect_num_outputs="1">
+        <conditional name="input_type">
+            <param name="input_type_selector" value="h5ad"/>
+            <param name="input_h5ad" location="https://zenodo.org/records/20029977/files/input.h5ad"/>
+            <param name="stem" value="h5ad"/>
+            <section name="sec_advanced_options">
+                <conditional name="var_subset_conditional">
+                    <param name="var_subset" value="true"/>
+                    <param name="var_subset_column" value="gene_ids"/>
+                    <param name="var_subset_values" value="A1CF,MSN"/>
+                </conditional>
+            </section>
+        </conditional>
+        <output name="output_zarr">
+            <extra_files type="file" name="h5ad-anndata.zarr/.zmetadata">
+                <assert_contents>
+                    <has_text text="&quot;zarr_format&quot;: 2"/>
+                    <has_text text="&quot;cname&quot;: &quot;lz4&quot;"/>
+                    <has_text text="&quot;id&quot;: &quot;blosc&quot;"/>
+                </assert_contents>
+            </extra_files>
+        </output>
+    </test>
+
+    <test expect_num_outputs="1">
+        <conditional name="input_type">
+            <param name="input_type_selector" value="h5ad"/>
+            <param name="input_h5ad" location="https://zenodo.org/records/20029977/files/input.h5ad"/>
+            <param name="stem" value="h5ad"/>
+            <section name="sec_advanced_options">
+                <conditional name="obs_subset_conditional">
+                    <param name="obs_subset" value="true"/>
+                    <param name="obs_subset_column" value="in_tissue"/>
+                    <param name="obs_subset_values" value="1"/>
+                </conditional>
+                <conditional name="var_subset_conditional">
+                    <param name="var_subset" value="true"/>
+                    <param name="var_subset_column" value="gene_ids"/>
+                    <param name="var_subset_values" value="A1CF,MSN"/>
+                </conditional>
+            </section>
+        </conditional>
+        <output name="output_zarr">
+            <extra_files type="file" name="h5ad-anndata.zarr/.zmetadata">
+                <assert_contents>
+                    <has_text text="&quot;zarr_format&quot;: 2"/>
+                    <has_text text="&quot;cname&quot;: &quot;lz4&quot;"/>
+                    <has_text text="&quot;id&quot;: &quot;blosc&quot;"/>
+                </assert_contents>
+            </extra_files>
+        </output>
+    </test>
+
+    <test expect_num_outputs="1">
+        <conditional name="input_type">
+            <param name="input_type_selector" value="h5ad"/>
+            <param name="input_h5ad" location="https://zenodo.org/records/20029977/files/input.h5ad"/>
+            <param name="stem" value="h5ad"/>
+            <section name="sec_advanced_options">
+                <conditional name="batch_processing_conditional">
+                    <param name="batch_processing" value="true"/>
+                    <param name="batch_size" value="100"/>
+                </conditional>
+            </section>
+        </conditional>
+        <output name="output_zarr">
+            <extra_files type="file" name="h5ad-anndata.zarr/.zmetadata">
+                <assert_contents>
+                    <has_text text="&quot;zarr_format&quot;: 2"/>
+                    <has_text text="feature_types"/>
+                </assert_contents>
+            </extra_files>
+        </output>
+    </test>
+
+    <test expect_num_outputs="2">
+        <conditional name="input_type">
+            <param name="input_type_selector" value="spaceranger"/>
+            <param name="input_spaceranger" location="https://zenodo.org/records/20029977/files/spaceranger.zip"/>
+            <param name="stem" value="visium-breast-cancer"/>
+            <param name="save_h5ad" value="true"/>
+        </conditional>
+        <output name="output_zarr">
+            <extra_files type="file" name="visium-breast-cancer-anndata.zarr/.zmetadata">
+                <assert_contents>
+                    <has_text text="&quot;zarr_format&quot;: 2"/>
+                    <has_text text="feature_types"/>
+                </assert_contents>
+            </extra_files>
+        </output>
+        <output name="output_h5ad" ftype="h5ad">
+            <assert_contents>
+                <has_h5_keys keys="obs/array_row"/>
+                <has_h5_keys keys="obs/graphclust"/>
+                <has_h5_keys keys="uns/spatial"/>
+                <has_h5_keys keys="obsm/spatial"/>
+            </assert_contents>
+        </output>
+    </test>
+
+    <test expect_num_outputs="2">
+        <conditional name="input_type">
+            <param name="input_type_selector" value="xenium"/>
+            <param name="input_xenium" location="https://zenodo.org/records/20029977/files/Xenium_Prime_MultiCellSeg_Mouse_Ileum_tiny_outs.zip"/>
+            <param name="stem" value="xenium-tiny"/>
+            <param name="save_h5ad" value="true"/>
+        </conditional>
+        <output name="output_zarr">
+            <extra_files type="file" name="xenium-tiny-anndata.zarr/.zmetadata">
+                <assert_contents>
+                    <has_text text="&quot;zarr_format&quot;: 2"/>
+                    <has_text text="&quot;cname&quot;: &quot;lz4&quot;"/>
+                    <has_text text="&quot;id&quot;: &quot;blosc&quot;"/>
+                </assert_contents>
+            </extra_files>
+        </output>
+        <output name="output_h5ad" ftype="h5ad">
+            <assert_contents>
+                <has_h5_keys keys="obs/x_centroid"/>
+                <has_h5_keys keys="obsm/X_spatial"/>
+                <has_h5_keys keys="uns/xenium"/>
+            </assert_contents>
+        </output>
+    </test>
+
+    <test expect_num_outputs="2">
+        <conditional name="input_type">
+            <param name="input_type_selector" value="merscope"/>
+            <param name="input_merscope" location="https://zenodo.org/records/20029977/files/merscope.zip"/>
+            <param name="stem" value="merscope"/>
+            <param name="save_h5ad" value="true"/>
+        </conditional>
+        <output name="output_zarr">
+            <extra_files type="file" name="merscope-anndata.zarr/.zmetadata">
+                <assert_contents>
+                    <has_text text="&quot;zarr_format&quot;: 2"/>
+                    <has_text text="&quot;cname&quot;: &quot;lz4&quot;"/>
+                    <has_text text="&quot;id&quot;: &quot;blosc&quot;"/>
+                </assert_contents>
+            </extra_files>
+        </output>
+        <output name="output_h5ad" ftype="h5ad">
+            <assert_contents>
+                <has_h5_keys keys="obs/fov"/>
+                <has_h5_keys keys="obs/solidity"/>
+                <has_h5_keys keys="obs/perimeter_area_ratio"/>
+                <has_h5_keys keys="obsm/spatial"/>
+            </assert_contents>
+        </output>
+    </test>
+    </tests>
+    <help><![CDATA[
+This tool converts supported spatial omics data formats into an AnnData object and subsequently into the Zarr format.
+It is used to standardize spatial omics data formats, ensuring compatibility with downstream visualization.
+
+----
+
+**Supported Input Types**
+
+- **AnnData file (H5AD)**
+- **SpaceRanger output archive (ZIP)**
+- **Xenium output archive (ZIP)**
+- **MERSCOPE output archive (ZIP)**
+
+----
+
+**Processing Steps**
+
+Regardless of input type, the following steps are performed:
+
+- Conversion to AnnData (if input is not already AnnData)
+- Standardization of data types and structure
+- Optional preprocessing (e.g. subsetting, embeddings)
+- Conversion to Zarr format
+
+----
+
+**Parameters**
+
+- **Output Zarr column chunk size**
+    Defines how many variables (e.g. genes) are stored per chunk in the Zarr representation of the expression matrix.
+    A single chunk contains all observations (e.g. cells) and the specified amount of variables.
+    Smaller chunks can lead to more efficient data retrieval in downstream analysis and visualization when accessing a small number of variables.
+    Larger chunks may improve writing speed to the Zarr format and improve performance when accessing larger portions of the dataset at the same time.
+
+- **Compute embeddings**
+    If enabled, PCA and UMAP embeddings are computed from the AnnData object if they are not already present.
+    These embeddings are usually required for downstream visualization.
+
+- **Alternative var index**
+    Specifies an alternative column in the *var* table to be used as the primary feature index.
+    This allows the use of specific identifiers, such as gene names, when the default index does not contain the desired values.
+
+- **Batch processing and batch size**
+    Enables incremental processing of the AnnData into Zarr in batches defined by batch size.
+    This prevents loading the full dataset into memory at once, making it useful for large datasets.
+    This is a trade-off between memory usage and runtime. It does not change the structure of the final Zarr output.
+
+- **Subset AnnData on an obs column**
+    Allows filtering of observations based on a specified column in the *obs* table. Only observations matching the specified values are kept in the dataset.
+
+- **Subset AnnData on a var column**
+    Allows filtering of variables based on a specified column in the *var* table (e.g. gene_ids). Only variables matching the specified values (e.g. A1CF, MSN) are kept in the dataset.
+
+- **Consolidate metadata**
+    Whether the Zarr metadata is consolidated, which can improve read performance by reducing the amount of metadata files that need to be accessed.
+    Disabling this is usually only useful if specific metadata entries wish to be modified. Only disable this if you have a specific use in mind.
+
+----
+
+**Input type specific parameters**
+
+- **SpaceRanger**
+
+  - Include clustering files: Whether cluster files from the SpaceRanger data are included in the AnnData object.
+  - Include embeddings: Whether embeddings (e.g. PCA, UMAP) from the SpaceRanger data are included in the AnnData object.
+  - Use raw matrix count file: Loads the raw matrix count file instead of the filtered matrix file.
+
+- **Xenium**
+
+  - Convert spatial coordinates to pixel coordinates: Convert Xenium spatial coordinates to pixel coordinates using the specified pixel resolution.
+  - Pixel resolution: Pixel resolution used for converting Xenium spatial coordinates to pixel coordinates.
+
+- **MERSCOPE**
+
+  - Filter prefix: Prefix to filter out of the MERSCOPE data.
+
+----
+
+**Output**
+
+- **AnnData Zarr dataset**
+
+The output is used as input for the downstream WebAtlas tools **WebAtlas Build Vitessce Config** and **WebAtlas Write**.
+    ]]></help>
+    <expand macro="citations"/>
+</tool>
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diff --git a/tools/webatlas/write_spatialdata.xml b/tools/webatlas/write_spatialdata.xml
new file mode 100644
index 0000000000..955913849f
--- /dev/null
+++ b/tools/webatlas/write_spatialdata.xml
@@ -0,0 +1,133 @@
+<tool id="webatlas_write_spatialdata" name="WebAtlas Write" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" python_template_version="3.5" profile="@PROFILE_VERSION@">
+    <description>AnnData and images into SpatialData Zarr</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements"/>
+    <command detect_errors="exit_code"><![CDATA[
+        #if $input_anndata.ext =="h5ad":
+            cp '$input_anndata' input.h5ad &&
+        #end if
+        #if $input_raw_img
+            ln -s '$input_raw_img' raw_img.tif &&
+        #end if
+        #if $input_label_img
+            ln -s '$input_label_img' label_img.tif &&
+        #end if
+        write_spatialdata.py
+        #if $input_anndata.ext =="zarr":
+            --anndata_path '$input_anndata.extra_files_path/$input_anndata.metadata.store_root'
+        #else
+            --anndata_path input.h5ad
+        #end if
+        --stem '$stem'
+        #if $input_raw_img
+            --raw_img_path raw_img.tif
+        #end if
+        #if $input_label_img
+            --label_img_path label_img.tif
+        #end if
+        &&
+        zip -r '$stem-spatialdata.zarr.zip' '$stem-spatialdata.zarr' &&
+        mv '$stem-spatialdata.zarr.zip' '$output_zarr'
+    ]]></command>
+    <inputs>
+        <param name="input_anndata" type="data" format="h5ad,zarr" label="AnnData input" help="AnnData input to include in the SpatialData Zarr. Can be H5AD or AnnData Zarr."/>
+        <expand macro="stem"/>
+        <param name="input_raw_img" type="data" format="tif,tiff" optional="true" label="Raw image TIFF" help="Optional raw TIFF image to include in the SpatialData Zarr."/>
+        <param name="input_label_img" type="data" format="tif,tiff" optional="true" label="Label image TIFF" help="Optional label TIFF image to include in the SpatialData Zarr."/>
+    </inputs>
+    <outputs>
+        <data name="output_zarr" format="zarr.zip" label="${tool.name} on ${on_string}: ZIP-compressed SpatialData Zarr output"/>
+    </outputs>
+    <tests>
+        <test expect_num_outputs="1">
+            <param name="input_anndata" location="https://zenodo.org/records/20029977/files/visium-breast-cancer-anndata.zarr.zip"/>
+            <param name="stem" value="visium-breast-cancer"/>
+            <param name="input_raw_img" location="https://zenodo.org/records/20029977/files/tissue_image.tif"/>
+            <param name="input_label_img" location="https://zenodo.org/records/20029977/files/visium-breast-cancer-label.tif"/>
+            <output name="output_zarr">
+                <assert_contents>
+                    <has_archive_member path="visium-breast-cancer-spatialdata.zarr/.zgroup"/>
+                    <has_archive_member path="visium-breast-cancer-spatialdata.zarr/.zattrs"/>
+                    <has_archive_member path="visium-breast-cancer-spatialdata.zarr/tables/.zgroup"/>
+                    <has_archive_member path="visium-breast-cancer-spatialdata.zarr/images/raw/.zgroup"/>
+                    <has_archive_member path="visium-breast-cancer-spatialdata.zarr/labels/label/.zgroup"/>
+                    <has_size value="936976652" delta="20000"/>
+                </assert_contents>
+            </output>
+        </test>
+        <test expect_num_outputs="1">
+            <param name="input_anndata" location="https://zenodo.org/records/20029977/files/input.h5ad"/>
+            <param name="stem" value="visium-breast-cancer"/>
+            <param name="input_raw_img" location="https://zenodo.org/records/20029977/files/tissue_image.tif"/>
+            <param name="input_label_img" location="https://zenodo.org/records/20029977/files/visium-breast-cancer-label.tif"/>
+            <output name="output_zarr">
+                <assert_contents>
+                    <has_archive_member path="visium-breast-cancer-spatialdata.zarr/.zgroup"/>
+                    <has_archive_member path="visium-breast-cancer-spatialdata.zarr/.zattrs"/>
+                    <has_archive_member path="visium-breast-cancer-spatialdata.zarr/tables/.zgroup"/>
+                    <has_archive_member path="visium-breast-cancer-spatialdata.zarr/images/raw/.zgroup"/>
+                    <has_archive_member path="visium-breast-cancer-spatialdata.zarr/labels/label/.zgroup"/>
+                    <has_size value="928962769" delta="20000"/>
+                </assert_contents>
+            </output>
+        </test>
+        <test expect_num_outputs="1">
+            <param name="input_anndata" location="https://zenodo.org/records/20029977/files/visium-breast-cancer-anndata.zarr.zip"/>
+            <param name="stem" value="visium-breast-cancer"/>
+            <output name="output_zarr">
+                <assert_contents>
+                    <has_archive_member path="visium-breast-cancer-spatialdata.zarr/.zgroup"/>
+                    <has_archive_member path="visium-breast-cancer-spatialdata.zarr/.zattrs"/>
+                    <has_archive_member path="visium-breast-cancer-spatialdata.zarr/tables/.zgroup"/>
+                    <has_size value="77147714" delta="20000"/>
+                </assert_contents>
+            </output>
+        </test>
+    </tests>
+    <help><![CDATA[
+This tool converts spatial omics data into a SpatialData object and exports it as a Zarr dataset.
+
+----
+
+**Inputs**
+
+- **AnnData** (H5AD or Zarr)
+- **Label image (TIFF)** *(optional)*
+- **Raw image (TIFF)** *(optional)*
+
+Image inputs can be provided independently or omitted entirely.
+
+----
+
+**Functionality**
+
+The tool constructs a SpatialData object from the provided inputs:
+
+- The AnnData object is stored as a **table element**
+- The label image is stored as a **labels element**
+- The raw image is stored as an **image element**
+
+To ensure compatibility with the SpatialData format, the observation index of the AnnData object is adjusted.
+A new integer-based index *webatlas_index* is introduced while preserving the original observation index as *original_obs_index*.
+
+The resulting SpatialData object is written to Zarr format.
+
+----
+
+**Output**
+
+- **SpatialData object (Zarr, ZIP-compressed)**
+
+----
+
+**Use Case**
+
+This SpatialData object enables unified storage and handling of different types of spatial omics data (e.g. AnnData, label images, raw images) in a single data structure.
+It can be used in other tools or workflows that support SpatialData in Zarr format.
+
+SpatialData objects are not utilized by the WebAtlas pipeline itself.
+    ]]></help>
+    <expand macro="citations"/>
+</tool>
\ No newline at end of file