From efa224bcaf59ef7004102f2deffc324d71161aec Mon Sep 17 00:00:00 2001 From: Pavankumar Videm Date: Mon, 13 Apr 2026 09:38:55 +0200 Subject: [PATCH 01/20] Update title and the intro --- index-spatialomics.md | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/index-spatialomics.md b/index-spatialomics.md index 1c2f9cd90..b04c782b4 100644 --- a/index-spatialomics.md +++ b/index-spatialomics.md @@ -4,12 +4,14 @@ website: https://spatialomics.usegalaxy.eu subdomain: spatialomics --- -# Welcome to the Spatial OMICS Galaxy subdomain server +# Welcome to the Spatial OMICS Galaxy server {:.no_toc} ![](/assets/media/spatial_omics_banner.jpg) -The SpatialOMICS Galaxy subdomain serves as a hub for all tools related to the analysis of highly-multiplexed image analysis. This server currently features the individual components of the [MCMICRO](https://mcmicro.org/) pipeline, including [BaSiC](https://github.com/ohsu-comp-bio/basic-illumination) for illumination correction, [ASHLAR](https://github.com/ohsu-comp-bio/ashlar) for stitching and registration, [Coreograph](https://github.com/ohsu-comp-bio/UNetCoreograph) to dearray tissue microarrays (TMAs), [UnMICST](https://github.com/ohsu-comp-bio/UnMicst) to create cell or nucleai probability maps, [S3segmenter](https://github.com/ohsu-comp-bio/S3segmenter) for nucleai and cell segmentation and [MCQuant](https://github.com/ohsu-comp-bio/quantification) for feature quantification. More tools for image analysis outside the MCMICRO ecosystem will be added in the future. +The SpatialOMICS Galaxy server is a hub for all tools related to the analysis of highly multiplexed image-based spatial analysis. + +This server currently features the individual components of the [MCMICRO](https://mcmicro.org/) pipeline, including [BaSiC](https://github.com/ohsu-comp-bio/basic-illumination) for illumination correction, [ASHLAR](https://github.com/ohsu-comp-bio/ashlar) for stitching and registration, [Coreograph](https://github.com/ohsu-comp-bio/UNetCoreograph) to dearray tissue microarrays (TMAs), [UnMICST](https://github.com/ohsu-comp-bio/UnMicst) to create cell or nucleai probability maps, [S3segmenter](https://github.com/ohsu-comp-bio/S3segmenter) for nucleai and cell segmentation and [MCQuant](https://github.com/ohsu-comp-bio/quantification) for feature quantification. More tools for image analysis outside the MCMICRO ecosystem will be added in the future. This subdomain is a collaborative effort and we welcome any suggestions or requests for making tools related to spatia OMICS analysis available on this server. We also welcome contributions to the development of new tools, workflows or trainings! From d1366b79c95a3aac57784043eda00a1216b643c7 Mon Sep 17 00:00:00 2001 From: Pavankumar Videm Date: Tue, 21 Apr 2026 15:52:58 +0200 Subject: [PATCH 02/20] Add SpatialData tools section to documentation Added SpatialData section with tools and references for handling spatial omics data. --- index-spatialomics.md | 10 ++++++++++ 1 file changed, 10 insertions(+) diff --git a/index-spatialomics.md b/index-spatialomics.md index b04c782b4..761b49245 100644 --- a/index-spatialomics.md +++ b/index-spatialomics.md @@ -29,6 +29,16 @@ Take [a guided tour]({{ page.website }}/tours/core.galaxy_ui){:target="_blank"} # Tools available +## SpatialData + +The SpatialData datatype and utilities for reading, writing, manipulating and plotting SpatialData objects have been developed as part of [Spatial2Galaxy CMR project](https://elixir-europe.org/how-we-work/scientific-programme/science/cmr/spatial2). + +Tool | Description | Reference +--- | --- | --- +{% include tool.html id="spatialdata_io" %} | Load common spatial omics formats into SpatialData| [Marconato et al. 2024](https://doi.org/10.1038/s41592-024-02212-x){:target="_blank"}, [spatialdata Github](https://github.com/scverse/spatialdata){:target="_blank"} +{% include tool.html id="spatialdata_operation" %} | Perform operations on SpatialData objects | [Marconato et al. 2024](https://doi.org/10.1038/s41592-024-02212-x){:target="_blank"},[spatialdata Github](https://github.com/scverse/spatialdata){:target="_blank"} +{% include tool.html id="spatialdata_plot" %} | Rich static plotting from SpatialData objects | [Marconato et al. 2024](https://doi.org/10.1038/s41592-024-02212-x){:target="_blank"}, [spatialdata-plot Github](https://github.com/scverse/spatialdata-plot){:target="_blank"} + ## MCMICRO core tools All of the Galaxy tools for MCMICRO have been developed by the [Goecks lab](https://www.ohsu.edu/people/jeremy-goecks-phd) at the [Oregon Health and Science University Computational Biology](https://github.com/ohsu-comp-bio). From 7f07fd02895602995a75b19825bc69cd96a16299 Mon Sep 17 00:00:00 2001 From: Pavankumar Videm Date: Wed, 22 Apr 2026 11:47:31 +0200 Subject: [PATCH 03/20] Add files via upload --- assets/media/spatial2galaxy.svg | 541 ++++++++++++++++++++++++++++++++ 1 file changed, 541 insertions(+) create mode 100644 assets/media/spatial2galaxy.svg diff --git a/assets/media/spatial2galaxy.svg b/assets/media/spatial2galaxy.svg new file mode 100644 index 000000000..a58bbff30 --- /dev/null +++ b/assets/media/spatial2galaxy.svg @@ -0,0 +1,541 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + From 9c493b57e7e5eec758b42c0da9ca9d51dce820fa Mon Sep 17 00:00:00 2001 From: Pavankumar Videm Date: Wed, 22 Apr 2026 12:22:02 +0200 Subject: [PATCH 04/20] Enhance content and add S2G in partner/supporter sections Expanded the introduction to include collaboration details and contributions. Added sections for Spatial2Galaxy Partners and Supporters with relevant information. Added S2G logo. --- index-spatialomics.md | 26 +++++++++++++++++++++++--- 1 file changed, 23 insertions(+), 3 deletions(-) diff --git a/index-spatialomics.md b/index-spatialomics.md index 761b49245..f3de32fe1 100644 --- a/index-spatialomics.md +++ b/index-spatialomics.md @@ -9,11 +9,10 @@ subdomain: spatialomics ![](/assets/media/spatial_omics_banner.jpg) -The SpatialOMICS Galaxy server is a hub for all tools related to the analysis of highly multiplexed image-based spatial analysis. +The SpatialOMICS Galaxy server is a hub for all tools related to the analysis of highly multiplexed image-based spatial analysis. This subdomain is a collaborative effort and we welcome any suggestions or requests for making tools related to spatia OMICS analysis available on this server. We also welcome contributions to the development of new tools, workflows or trainings! -This server currently features the individual components of the [MCMICRO](https://mcmicro.org/) pipeline, including [BaSiC](https://github.com/ohsu-comp-bio/basic-illumination) for illumination correction, [ASHLAR](https://github.com/ohsu-comp-bio/ashlar) for stitching and registration, [Coreograph](https://github.com/ohsu-comp-bio/UNetCoreograph) to dearray tissue microarrays (TMAs), [UnMICST](https://github.com/ohsu-comp-bio/UnMicst) to create cell or nucleai probability maps, [S3segmenter](https://github.com/ohsu-comp-bio/S3segmenter) for nucleai and cell segmentation and [MCQuant](https://github.com/ohsu-comp-bio/quantification) for feature quantification. More tools for image analysis outside the MCMICRO ecosystem will be added in the future. -This subdomain is a collaborative effort and we welcome any suggestions or requests for making tools related to spatia OMICS analysis available on this server. We also welcome contributions to the development of new tools, workflows or trainings! +This server currently features the individual components of the [MCMICRO](https://mcmicro.org/) pipeline, including [BaSiC](https://github.com/ohsu-comp-bio/basic-illumination) for illumination correction, [ASHLAR](https://github.com/ohsu-comp-bio/ashlar) for stitching and registration, [Coreograph](https://github.com/ohsu-comp-bio/UNetCoreograph) to dearray tissue microarrays (TMAs), [UnMICST](https://github.com/ohsu-comp-bio/UnMicst) to create cell or nucleai probability maps, [S3segmenter](https://github.com/ohsu-comp-bio/S3segmenter) for nucleai and cell segmentation and [MCQuant](https://github.com/ohsu-comp-bio/quantification) for feature quantification. More tools for image analysis outside the MCMICRO ecosystem will be added in the future. # Content {:.no_toc} @@ -69,3 +68,24 @@ Two workflows are currently available to process your samples using the MCMICRO - [Jeremy Goecks](https://github.com/jgoecks) - [Cameron Watson](https://github.com/CameronFRWatson) - [Allison Creason](https://github.com/alliecreason) + +# Spatial2Galaxy Partners + +| Partners | Description | People involved | +|----------|-------------|-----------------| +| [Erasmus Medical Center](https://www.erasmusmc.nl/en/research/groups/pathology-stubbs) | Example description | Andrew Stubbs +| [Berlin Institute of Health at Charité](https://www.hidih.org/research/computational-oncology) | Example description | Naveed Ishaque +| [University of Bradford] (https://www.bradford.ac.uk) | Example description | Krzysztof Poterlowicz +| [University of Freiburg] (https://usegalaxy-eu.github.io/people) | Example description | Björn Grüning +{:.table.table-striped} + + +# Supporters +This service is a joint project between different groups from the [Spatial2Galaxy](https://elixir-europe.org/how-we-work/scientific-programme/science/cmr/spatial2){:target="_blank"}, an ELIXIR Cellular and molecular research project, [The Goecks Laboratory](https://www.goeckslab.org/). + + +
+Spatial2Galaxy + +ELIXIR +
From da0ccdb9186f848f25b5991d0738a9b8ce37331c Mon Sep 17 00:00:00 2001 From: Pavankumar Videm Date: Wed, 22 Apr 2026 18:33:19 +0200 Subject: [PATCH 05/20] Add more plotting tools and update logo --- assets/media/spatial2galaxy.svg | 1090 ++++++++++++++++++------------- index-spatialomics.md | 33 +- 2 files changed, 673 insertions(+), 450 deletions(-) diff --git a/assets/media/spatial2galaxy.svg b/assets/media/spatial2galaxy.svg index a58bbff30..fe583bf0c 100644 --- a/assets/media/spatial2galaxy.svg +++ b/assets/media/spatial2galaxy.svg @@ -2,9 +2,9 @@ + + + + + + + + @@ -84,458 +108,640 @@ x2="101.72906" y2="76.316841" gradientUnits="userSpaceOnUse" /> + + + + - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - + transform="translate(-99.757276,-48.39368)"> + id="g58440" + transform="translate(-0.05713373)"> - - - - + id="path59285" + style="font-weight:bold;font-size:28.6698px;line-height:1.25;-inkscape-font-specification:'sans-serif Bold';fill:#ff770b;fill-opacity:1;stroke-width:1.13379" + d="m 141.46444,62.073941 -0.82154,-2.343075 c -1.54731,1.935275 -3.66638,3.845736 -5.8679,5.180792 l 0.92871,2.307007 c 2.15334,-1.460203 4.13104,-3.262224 5.76073,-5.144724 z" + sodipodi:nodetypes="ccccc" /> + aria-label="G" + id="text41182" + style="font-weight:bold;font-size:26.4125px;line-height:1.25;font-family:FreeMono;-inkscape-font-specification:FreeMono;fill:#58585a;fill-opacity:1;stroke-width:0.328666" + transform="matrix(1.0315828,0,0,1.0315828,-33.154291,-0.70183813)"> - 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- + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/index-spatialomics.md b/index-spatialomics.md index f3de32fe1..c7a31bb1e 100644 --- a/index-spatialomics.md +++ b/index-spatialomics.md @@ -28,15 +28,28 @@ Take [a guided tour]({{ page.website }}/tours/core.galaxy_ui){:target="_blank"} # Tools available -## SpatialData +## Spatial Datatypes and Utilities The SpatialData datatype and utilities for reading, writing, manipulating and plotting SpatialData objects have been developed as part of [Spatial2Galaxy CMR project](https://elixir-europe.org/how-we-work/scientific-programme/science/cmr/spatial2). -Tool | Description | Reference ---- | --- | --- -{% include tool.html id="spatialdata_io" %} | Load common spatial omics formats into SpatialData| [Marconato et al. 2024](https://doi.org/10.1038/s41592-024-02212-x){:target="_blank"}, [spatialdata Github](https://github.com/scverse/spatialdata){:target="_blank"} -{% include tool.html id="spatialdata_operation" %} | Perform operations on SpatialData objects | [Marconato et al. 2024](https://doi.org/10.1038/s41592-024-02212-x){:target="_blank"},[spatialdata Github](https://github.com/scverse/spatialdata){:target="_blank"} -{% include tool.html id="spatialdata_plot" %} | Rich static plotting from SpatialData objects | [Marconato et al. 2024](https://doi.org/10.1038/s41592-024-02212-x){:target="_blank"}, [spatialdata-plot Github](https://github.com/scverse/spatialdata-plot){:target="_blank"} +Tool | Description +--- | --- +{% include tool.html id="spatialdata_io" %} | Load common spatial omics formats into SpatialData +{% include tool.html id="spatialdata_operation" %} | Perform operations on SpatialData objects +{% include tool.html id="seurat_create" %} | Create Seurat objects from Xenium spatial data + +## Plotting and Visualization + +Tool | Description +--- | --- +{% include tool.html id="spatialdata_plot" %} | Rich static plotting from SpatialData objects +{% include tool.html id="seurat_plot" %} | Visualize spatial clusters and features from Seurat objects +{% include tool.html id="bellavista_prepare" %} | Prepare large images for bellavista spatial visualizer +{% include tool.html id="interactive_tool_bellavista" %} | Interactive visualization for imaging-based spatial transcriptomics +{% include tool.html id="squidpy_scatter" %} | Create spatial scatterplot with Squidpy +{% include tool.html id="interactive_tool_cellxgene_vip" %} | Interactive CELLxGENE VIP visualization for scRNA-seq, spatial transcriptomics, and multiome data +{% include tool.html id="interactive_tool_napari" %} | Interactive exploration and annotation of spatial omics data with napari + ## MCMICRO core tools @@ -68,6 +81,10 @@ Two workflows are currently available to process your samples using the MCMICRO - [Jeremy Goecks](https://github.com/jgoecks) - [Cameron Watson](https://github.com/CameronFRWatson) - [Allison Creason](https://github.com/alliecreason) +- [Amirhossein Nilchi](https://github.com/nilchia) +- [Khaled Jumah](https://github.com/khaled196) +- [Pavankumar Videm](https://github.com/pavanvidem) + # Spatial2Galaxy Partners @@ -75,8 +92,8 @@ Two workflows are currently available to process your samples using the MCMICRO |----------|-------------|-----------------| | [Erasmus Medical Center](https://www.erasmusmc.nl/en/research/groups/pathology-stubbs) | Example description | Andrew Stubbs | [Berlin Institute of Health at Charité](https://www.hidih.org/research/computational-oncology) | Example description | Naveed Ishaque -| [University of Bradford] (https://www.bradford.ac.uk) | Example description | Krzysztof Poterlowicz -| [University of Freiburg] (https://usegalaxy-eu.github.io/people) | Example description | Björn Grüning +| [University of Bradford](https://www.bradford.ac.uk) | Example description | Krzysztof Poterlowicz +| [University of Freiburg](https://usegalaxy-eu.github.io/people) | Example description | Björn Grüning {:.table.table-striped} From a1e1a0a5098ddea40364d6426f576e4acfd343d4 Mon Sep 17 00:00:00 2001 From: Pavankumar Videm Date: Tue, 12 May 2026 12:15:58 +0200 Subject: [PATCH 06/20] Add segmentation and preprocessing tools section with vpt --- index-spatialomics.md | 9 +++++++++ 1 file changed, 9 insertions(+) diff --git a/index-spatialomics.md b/index-spatialomics.md index c7a31bb1e..87c956a2f 100644 --- a/index-spatialomics.md +++ b/index-spatialomics.md @@ -38,6 +38,15 @@ Tool | Description {% include tool.html id="spatialdata_operation" %} | Perform operations on SpatialData objects {% include tool.html id="seurat_create" %} | Create Seurat objects from Xenium spatial data +## Segmentation and Preprocessing + +Several tools for segmenting and pre-processing the spatial transcriptomics data into SpatialData objects have been developed as part of [Spatial2Galaxy CMR project](https://elixir-europe.org/how-we-work/scientific-programme/science/cmr/spatial2). + +Tool | Description +--- | --- +{% include tool.html id="vpt_segment" %} | Vizgen VPT - Segment cells and refine MERSCOPE experiments +{% include tool.html id="vpt_extract" %} | Vizgen VPT - Extract image patches + ## Plotting and Visualization Tool | Description From d0e384d96e9195ee6522d882b7d4f1ce526033a1 Mon Sep 17 00:00:00 2001 From: Pavankumar Videm Date: Tue, 12 May 2026 15:26:28 +0200 Subject: [PATCH 07/20] Add more tools for downstream analysis --- index-spatialomics.md | 43 ++++++++++++++++++++++++++++++++++++------- 1 file changed, 36 insertions(+), 7 deletions(-) diff --git a/index-spatialomics.md b/index-spatialomics.md index 87c956a2f..238af3f2a 100644 --- a/index-spatialomics.md +++ b/index-spatialomics.md @@ -9,28 +9,29 @@ subdomain: spatialomics ![](/assets/media/spatial_omics_banner.jpg) -The SpatialOMICS Galaxy server is a hub for all tools related to the analysis of highly multiplexed image-based spatial analysis. This subdomain is a collaborative effort and we welcome any suggestions or requests for making tools related to spatia OMICS analysis available on this server. We also welcome contributions to the development of new tools, workflows or trainings! - +The SpatialOMICS Galaxy server is a hub for all tools related to the analysis of highly multiplexed image-based spatial analysis. This subdomain is a collaborative effort of Spatial2Galaxy and the Goecks Laboratory members. We welcome any suggestions or requests for making tools related to spatial OMICS analysis available on this server. We also welcome contributions to the development of new tools, workflows or trainings! This server currently features the individual components of the [MCMICRO](https://mcmicro.org/) pipeline, including [BaSiC](https://github.com/ohsu-comp-bio/basic-illumination) for illumination correction, [ASHLAR](https://github.com/ohsu-comp-bio/ashlar) for stitching and registration, [Coreograph](https://github.com/ohsu-comp-bio/UNetCoreograph) to dearray tissue microarrays (TMAs), [UnMICST](https://github.com/ohsu-comp-bio/UnMicst) to create cell or nucleai probability maps, [S3segmenter](https://github.com/ohsu-comp-bio/S3segmenter) for nucleai and cell segmentation and [MCQuant](https://github.com/ohsu-comp-bio/quantification) for feature quantification. More tools for image analysis outside the MCMICRO ecosystem will be added in the future. +Several spatial transcriptomics data formats and analysis tools have been integrated into Galaxy as part of the [Spatial2Galaxy CMR project](https://elixir-europe.org/how-we-work/scientific-programme/science/cmr/spatial2). + # Content {:.no_toc} 1. TOC {:toc} - # Get started Are you new to Galaxy, or returning after a long time, and looking for help to get started? Take [a guided tour]({{ page.website }}/tours/core.galaxy_ui){:target="_blank"} through Galaxy's user interface. # Tools available +Here, we outline all the Galaxy tools that are relevant in the context of spatial omics data analysis. ## Spatial Datatypes and Utilities -The SpatialData datatype and utilities for reading, writing, manipulating and plotting SpatialData objects have been developed as part of [Spatial2Galaxy CMR project](https://elixir-europe.org/how-we-work/scientific-programme/science/cmr/spatial2). +The `SpatialData` datatype and utilities for reading, writing, manipulating and plotting SpatialData objects. Tool | Description --- | --- @@ -40,12 +41,38 @@ Tool | Description ## Segmentation and Preprocessing -Several tools for segmenting and pre-processing the spatial transcriptomics data into SpatialData objects have been developed as part of [Spatial2Galaxy CMR project](https://elixir-europe.org/how-we-work/scientific-programme/science/cmr/spatial2). +Tools for segmenting and pre-processing the spatial transcriptomics data into SpatialData objects. Tool | Description --- | --- +{% include tool.html id="spapros_selection" %} | Selection of marker genes with spapros +{% include tool.html id="spapros_evaluation" %} | Evaluation of marker genes with spapros {% include tool.html id="vpt_segment" %} | Vizgen VPT - Segment cells and refine MERSCOPE experiments -{% include tool.html id="vpt_extract" %} | Vizgen VPT - Extract image patches +{% include tool.html id="vpt_extract" %} | Vizgen VPT - Extract image patches from the mosaic image at the specified coordinates and size + +## Spatial Downstream Analysis + +Tools for spatial transcriptomics downstream analysis + +Tool | Description +--- | --- +{% include tool.html id="squidpy_spatial" %} | Analyze and visualize spatial multi-omics data with Squidpy +{% include tool.html id="spacexr_rctd" %} | Robust Cell Type Decomposition, or RCTD, is a statistical method for learning cell types from spatial transcriptomics data +{% include tool.html id="spacexr_cside" %} | Cell type-Specific Inference of Differential Expression, or CSIDE, is part of the spacexr R package for learning cell type-specific differential expression from spatial transcriptomics data +{% include tool.html id="liana_methods" %} | Liana ligand_receptor inference and local bivariate spatial metrics for single-cell or spatial data +{% include tool.html id="liana_misty" %} | Liana MISTy learn spatial relationships with multi-view modelling +{% include tool.html id="liana_multi" %} | Liana multi-sample and multi-condition analysis +{% include tool.html id="liana_resource" %} | Liana Resource prior knowledge and ligand-receptor resources +{% include tool.html id="liana_utils" %} | LIANA utility functions for data transformation and preprocessing + +## Cell Annotation & Feature Selection + +Tools for marker gene identification and cell-type annotation + +Tool | Description +--- | --- +{% include tool.html id="cosg" %} | COSG is a cosine similarity-based method for more accurate and scalable marker gene identification +{% include tool.html id="celltypist" %}| CellTypist is an automated cell type annotation tool ## Plotting and Visualization @@ -58,7 +85,8 @@ Tool | Description {% include tool.html id="squidpy_scatter" %} | Create spatial scatterplot with Squidpy {% include tool.html id="interactive_tool_cellxgene_vip" %} | Interactive CELLxGENE VIP visualization for scRNA-seq, spatial transcriptomics, and multiome data {% include tool.html id="interactive_tool_napari" %} | Interactive exploration and annotation of spatial omics data with napari - +{% include tool.html id="vitessce_spatial" %} | Vitessce Visual Integration Tool for the Exploration of Spatial Single-Cell Experiments +{% include tool.html id="liana_plot" %} | Liana Plot visualize ligand-receptor interactions ## MCMICRO core tools @@ -73,6 +101,7 @@ Tool | Description | Reference {% include tool.html id="s3segmenter" %} | S3segmenter: A Matlab-based set of functions that generates single cell (nuclei and cytoplasm) label masks | [S3Segmenter github](https://github.com/HMS-IDAC/S3segmenter){:target="_blank"} {% include tool.html id="quantification" %} | MCQuant: Single cell quantification| [MCQUant github](https://github.com/labsyspharm/quantification#single-cell-quantification){:target="_blank"} +## Other tools # Workflows available From d615e3386ab807f35b1e9660a79901d794c97588 Mon Sep 17 00:00:00 2001 From: Pavankumar Videm Date: Tue, 12 May 2026 15:37:02 +0200 Subject: [PATCH 08/20] Remove 'Other tools' section from index-spatialomics Removed the 'Other tools' section from the document. --- index-spatialomics.md | 2 -- 1 file changed, 2 deletions(-) diff --git a/index-spatialomics.md b/index-spatialomics.md index 238af3f2a..c74b9407b 100644 --- a/index-spatialomics.md +++ b/index-spatialomics.md @@ -101,8 +101,6 @@ Tool | Description | Reference {% include tool.html id="s3segmenter" %} | S3segmenter: A Matlab-based set of functions that generates single cell (nuclei and cytoplasm) label masks | [S3Segmenter github](https://github.com/HMS-IDAC/S3segmenter){:target="_blank"} {% include tool.html id="quantification" %} | MCQuant: Single cell quantification| [MCQUant github](https://github.com/labsyspharm/quantification#single-cell-quantification){:target="_blank"} -## Other tools - # Workflows available Two workflows are currently available to process your samples using the MCMICRO Galaxy pipeline: From afe107bba684fde1f4884228d62f6294bdf70998 Mon Sep 17 00:00:00 2001 From: Pavankumar Videm Date: Tue, 12 May 2026 15:40:09 +0200 Subject: [PATCH 09/20] Add Nicola Soranzo to the contributors list --- index-spatialomics.md | 1 + 1 file changed, 1 insertion(+) diff --git a/index-spatialomics.md b/index-spatialomics.md index c74b9407b..2a7c70d6f 100644 --- a/index-spatialomics.md +++ b/index-spatialomics.md @@ -119,6 +119,7 @@ Two workflows are currently available to process your samples using the MCMICRO - [Allison Creason](https://github.com/alliecreason) - [Amirhossein Nilchi](https://github.com/nilchia) - [Khaled Jumah](https://github.com/khaled196) +- [Nicola Soranzo](https://github.com/nsoranzo) - [Pavankumar Videm](https://github.com/pavanvidem) From cf9ff01834ea0faa16dc39c542a0b38bd544ef63 Mon Sep 17 00:00:00 2001 From: Pavankumar Videm Date: Tue, 12 May 2026 15:50:05 +0200 Subject: [PATCH 10/20] Update partner descriptions in spatialomics index --- index-spatialomics.md | 9 +++++---- 1 file changed, 5 insertions(+), 4 deletions(-) diff --git a/index-spatialomics.md b/index-spatialomics.md index 2a7c70d6f..24da96df3 100644 --- a/index-spatialomics.md +++ b/index-spatialomics.md @@ -127,10 +127,11 @@ Two workflows are currently available to process your samples using the MCMICRO | Partners | Description | People involved | |----------|-------------|-----------------| -| [Erasmus Medical Center](https://www.erasmusmc.nl/en/research/groups/pathology-stubbs) | Example description | Andrew Stubbs -| [Berlin Institute of Health at Charité](https://www.hidih.org/research/computational-oncology) | Example description | Naveed Ishaque -| [University of Bradford](https://www.bradford.ac.uk) | Example description | Krzysztof Poterlowicz -| [University of Freiburg](https://usegalaxy-eu.github.io/people) | Example description | Björn Grüning +| [Berlin Institute of Health at Charité](https://www.hidih.org/research/computational-oncology) | Catalogue ST toolset and use cases | Naveed Ishaque +| [Erasmus Medical Center](https://www.erasmusmc.nl/en/research/groups/pathology-stubbs) | Implementation and validation of ST toolset | Andrew Stubbs +| [University of Bradford](https://www.bradford.ac.uk) | Develop Spatial2Galaxy tutorial suite and deliver training | Krzysztof Poterlowicz +| [University of Freiburg](https://usegalaxy-eu.github.io/people) | Development of Spatial2Galaxy portal, and support tool and workflow development | Björn Grüning +| [Earlham Institute](https://www.earlham.ac.uk/scientific-group/papatheodorou-group) | Develop Galaxy Demonstrator user case | Irene Papatheodorou {:.table.table-striped} From 99658ff1e87c1b67471c456b7e8774e7d53164b7 Mon Sep 17 00:00:00 2001 From: Pavankumar Videm Date: Tue, 12 May 2026 15:51:09 +0200 Subject: [PATCH 11/20] Update link for University of Freiburg in table --- index-spatialomics.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/index-spatialomics.md b/index-spatialomics.md index 24da96df3..9ddafc959 100644 --- a/index-spatialomics.md +++ b/index-spatialomics.md @@ -130,7 +130,7 @@ Two workflows are currently available to process your samples using the MCMICRO | [Berlin Institute of Health at Charité](https://www.hidih.org/research/computational-oncology) | Catalogue ST toolset and use cases | Naveed Ishaque | [Erasmus Medical Center](https://www.erasmusmc.nl/en/research/groups/pathology-stubbs) | Implementation and validation of ST toolset | Andrew Stubbs | [University of Bradford](https://www.bradford.ac.uk) | Develop Spatial2Galaxy tutorial suite and deliver training | Krzysztof Poterlowicz -| [University of Freiburg](https://usegalaxy-eu.github.io/people) | Development of Spatial2Galaxy portal, and support tool and workflow development | Björn Grüning +| [University of Freiburg](https://galaxyproject.org/freiburg/people/) | Development of Spatial2Galaxy portal, and support tool and workflow development | Björn Grüning | [Earlham Institute](https://www.earlham.ac.uk/scientific-group/papatheodorou-group) | Develop Galaxy Demonstrator user case | Irene Papatheodorou {:.table.table-striped} From a76c01090fde75f7f05bdf54bab223a149e64a62 Mon Sep 17 00:00:00 2001 From: Pavankumar Videm Date: Wed, 13 May 2026 10:22:05 +0200 Subject: [PATCH 12/20] reorder S2G partners list --- index-spatialomics.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/index-spatialomics.md b/index-spatialomics.md index 9ddafc959..89c695a77 100644 --- a/index-spatialomics.md +++ b/index-spatialomics.md @@ -127,8 +127,8 @@ Two workflows are currently available to process your samples using the MCMICRO | Partners | Description | People involved | |----------|-------------|-----------------| -| [Berlin Institute of Health at Charité](https://www.hidih.org/research/computational-oncology) | Catalogue ST toolset and use cases | Naveed Ishaque | [Erasmus Medical Center](https://www.erasmusmc.nl/en/research/groups/pathology-stubbs) | Implementation and validation of ST toolset | Andrew Stubbs +| [Berlin Institute of Health at Charité](https://www.hidih.org/research/computational-oncology) | Catalogue ST toolset and use cases | Naveed Ishaque | [University of Bradford](https://www.bradford.ac.uk) | Develop Spatial2Galaxy tutorial suite and deliver training | Krzysztof Poterlowicz | [University of Freiburg](https://galaxyproject.org/freiburg/people/) | Development of Spatial2Galaxy portal, and support tool and workflow development | Björn Grüning | [Earlham Institute](https://www.earlham.ac.uk/scientific-group/papatheodorou-group) | Develop Galaxy Demonstrator user case | Irene Papatheodorou From aaee7d9da505a38a55ac14d4952a7d18b5ab5cdf Mon Sep 17 00:00:00 2001 From: Pavankumar Videm Date: Wed, 13 May 2026 10:23:21 +0200 Subject: [PATCH 13/20] Fix formatting of partners table in index-spatialomics.md --- index-spatialomics.md | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/index-spatialomics.md b/index-spatialomics.md index 89c695a77..d0ea0d1fb 100644 --- a/index-spatialomics.md +++ b/index-spatialomics.md @@ -127,11 +127,11 @@ Two workflows are currently available to process your samples using the MCMICRO | Partners | Description | People involved | |----------|-------------|-----------------| -| [Erasmus Medical Center](https://www.erasmusmc.nl/en/research/groups/pathology-stubbs) | Implementation and validation of ST toolset | Andrew Stubbs -| [Berlin Institute of Health at Charité](https://www.hidih.org/research/computational-oncology) | Catalogue ST toolset and use cases | Naveed Ishaque -| [University of Bradford](https://www.bradford.ac.uk) | Develop Spatial2Galaxy tutorial suite and deliver training | Krzysztof Poterlowicz -| [University of Freiburg](https://galaxyproject.org/freiburg/people/) | Development of Spatial2Galaxy portal, and support tool and workflow development | Björn Grüning -| [Earlham Institute](https://www.earlham.ac.uk/scientific-group/papatheodorou-group) | Develop Galaxy Demonstrator user case | Irene Papatheodorou +| [Erasmus Medical Center](https://www.erasmusmc.nl/en/research/groups/pathology-stubbs) | Implementation and validation of ST toolset | Andrew Stubbs | +| [Berlin Institute of Health at Charité](https://www.hidih.org/research/computational-oncology) | Catalogue ST toolset and use cases | Naveed Ishaque | +| [University of Bradford](https://www.bradford.ac.uk) | Develop Spatial2Galaxy tutorial suite and deliver training | Krzysztof Poterlowicz | +| [University of Freiburg](https://galaxyproject.org/freiburg/people/) | Development of Spatial2Galaxy portal, and support tool and workflow development | Björn Grüning | +| [Earlham Institute](https://www.earlham.ac.uk/scientific-group/papatheodorou-group) | Develop Galaxy Demonstrator user case | Irene Papatheodorou | {:.table.table-striped} From 3fcd53bf636f1e0c02e243a4d7da2903d39ef0f7 Mon Sep 17 00:00:00 2001 From: Pavankumar Videm Date: Wed, 13 May 2026 13:21:38 +0200 Subject: [PATCH 14/20] Update index-spatialomics.md Co-authored-by: Nicola Soranzo --- index-spatialomics.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/index-spatialomics.md b/index-spatialomics.md index d0ea0d1fb..09a557e5d 100644 --- a/index-spatialomics.md +++ b/index-spatialomics.md @@ -9,7 +9,7 @@ subdomain: spatialomics ![](/assets/media/spatial_omics_banner.jpg) -The SpatialOMICS Galaxy server is a hub for all tools related to the analysis of highly multiplexed image-based spatial analysis. This subdomain is a collaborative effort of Spatial2Galaxy and the Goecks Laboratory members. We welcome any suggestions or requests for making tools related to spatial OMICS analysis available on this server. We also welcome contributions to the development of new tools, workflows or trainings! +The Spatial Omics Galaxy Lab is a hub for all tools related to the analysis of highly multiplexed image-based spatial analysis. This is a collaborative effort by the Spatial2Galaxy project and the Goecks Laboratory members. We welcome any suggestions or requests for making tools related to Spatial Omics analysis available on this Galaxy instance. We also welcome contributions to the development of new tools, workflows or trainings! This server currently features the individual components of the [MCMICRO](https://mcmicro.org/) pipeline, including [BaSiC](https://github.com/ohsu-comp-bio/basic-illumination) for illumination correction, [ASHLAR](https://github.com/ohsu-comp-bio/ashlar) for stitching and registration, [Coreograph](https://github.com/ohsu-comp-bio/UNetCoreograph) to dearray tissue microarrays (TMAs), [UnMICST](https://github.com/ohsu-comp-bio/UnMicst) to create cell or nucleai probability maps, [S3segmenter](https://github.com/ohsu-comp-bio/S3segmenter) for nucleai and cell segmentation and [MCQuant](https://github.com/ohsu-comp-bio/quantification) for feature quantification. More tools for image analysis outside the MCMICRO ecosystem will be added in the future. From cbe27dffa6d0a4babc409468332de76bb6239695 Mon Sep 17 00:00:00 2001 From: Pavankumar Videm Date: Wed, 13 May 2026 13:23:01 +0200 Subject: [PATCH 15/20] Update index-spatialomics.md Co-authored-by: Nicola Soranzo --- index-spatialomics.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/index-spatialomics.md b/index-spatialomics.md index 09a557e5d..a670b338e 100644 --- a/index-spatialomics.md +++ b/index-spatialomics.md @@ -13,7 +13,7 @@ The Spatial Omics Galaxy Lab is a hub for all tools related to the analysis of h This server currently features the individual components of the [MCMICRO](https://mcmicro.org/) pipeline, including [BaSiC](https://github.com/ohsu-comp-bio/basic-illumination) for illumination correction, [ASHLAR](https://github.com/ohsu-comp-bio/ashlar) for stitching and registration, [Coreograph](https://github.com/ohsu-comp-bio/UNetCoreograph) to dearray tissue microarrays (TMAs), [UnMICST](https://github.com/ohsu-comp-bio/UnMicst) to create cell or nucleai probability maps, [S3segmenter](https://github.com/ohsu-comp-bio/S3segmenter) for nucleai and cell segmentation and [MCQuant](https://github.com/ohsu-comp-bio/quantification) for feature quantification. More tools for image analysis outside the MCMICRO ecosystem will be added in the future. -Several spatial transcriptomics data formats and analysis tools have been integrated into Galaxy as part of the [Spatial2Galaxy CMR project](https://elixir-europe.org/how-we-work/scientific-programme/science/cmr/spatial2). +Several spatial transcriptomics data formats and analysis tools have been integrated into Galaxy as part of the [Spatial2Galaxy ELIXIR Commissioned Service](https://elixir-europe.org/how-we-work/scientific-programme/science/cmr/spatial2). # Content {:.no_toc} From 346c0a361d7187aa5645a66ddd6a0d02185df9c2 Mon Sep 17 00:00:00 2001 From: Pavankumar Videm Date: Wed, 13 May 2026 13:23:11 +0200 Subject: [PATCH 16/20] Update index-spatialomics.md Co-authored-by: Nicola Soranzo --- index-spatialomics.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/index-spatialomics.md b/index-spatialomics.md index a670b338e..45ea1a0b1 100644 --- a/index-spatialomics.md +++ b/index-spatialomics.md @@ -52,7 +52,7 @@ Tool | Description ## Spatial Downstream Analysis -Tools for spatial transcriptomics downstream analysis +Tools for spatial transcriptomics downstream analysis: Tool | Description --- | --- From 133686c013e85ed7e1b59b6d768ae1d7221112bc Mon Sep 17 00:00:00 2001 From: Pavankumar Videm Date: Wed, 13 May 2026 13:23:28 +0200 Subject: [PATCH 17/20] Update index-spatialomics.md Co-authored-by: Nicola Soranzo --- index-spatialomics.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/index-spatialomics.md b/index-spatialomics.md index 45ea1a0b1..183d0b937 100644 --- a/index-spatialomics.md +++ b/index-spatialomics.md @@ -136,7 +136,7 @@ Two workflows are currently available to process your samples using the MCMICRO # Supporters -This service is a joint project between different groups from the [Spatial2Galaxy](https://elixir-europe.org/how-we-work/scientific-programme/science/cmr/spatial2){:target="_blank"}, an ELIXIR Cellular and molecular research project, [The Goecks Laboratory](https://www.goeckslab.org/). +This Galaxy Lab is a joint project between different groups from the [Spatial2Galaxy ELIXIR Commissioned Service](https://elixir-europe.org/how-we-work/scientific-programme/science/cmr/spatial2){:target="_blank"} and the [Goecks Laboratory](https://www.goeckslab.org/). From e536d20f9bf6d914ed0c64c84baddf02f5266acc Mon Sep 17 00:00:00 2001 From: Pavankumar Videm Date: Wed, 13 May 2026 13:23:36 +0200 Subject: [PATCH 18/20] Update index-spatialomics.md Co-authored-by: Nicola Soranzo --- index-spatialomics.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/index-spatialomics.md b/index-spatialomics.md index 183d0b937..367064194 100644 --- a/index-spatialomics.md +++ b/index-spatialomics.md @@ -31,7 +31,7 @@ Here, we outline all the Galaxy tools that are relevant in the context of spatia ## Spatial Datatypes and Utilities -The `SpatialData` datatype and utilities for reading, writing, manipulating and plotting SpatialData objects. +The `SpatialData` datatype and utilities for reading, writing, manipulating and plotting SpatialData objects: Tool | Description --- | --- From d5c5bcc201c166b18073d353bc91fdf82126a3eb Mon Sep 17 00:00:00 2001 From: Pavankumar Videm Date: Wed, 13 May 2026 13:23:45 +0200 Subject: [PATCH 19/20] Update index-spatialomics.md Co-authored-by: Nicola Soranzo --- index-spatialomics.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/index-spatialomics.md b/index-spatialomics.md index 367064194..ec29bc7c3 100644 --- a/index-spatialomics.md +++ b/index-spatialomics.md @@ -41,7 +41,7 @@ Tool | Description ## Segmentation and Preprocessing -Tools for segmenting and pre-processing the spatial transcriptomics data into SpatialData objects. +Tools for segmenting and pre-processing the spatial transcriptomics data into SpatialData objects: Tool | Description --- | --- From fdee09904d9188b50ba9205c913521a96191d150 Mon Sep 17 00:00:00 2001 From: Pavankumar Videm Date: Wed, 13 May 2026 13:23:53 +0200 Subject: [PATCH 20/20] Update index-spatialomics.md Co-authored-by: Nicola Soranzo --- index-spatialomics.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/index-spatialomics.md b/index-spatialomics.md index ec29bc7c3..37e921b55 100644 --- a/index-spatialomics.md +++ b/index-spatialomics.md @@ -67,7 +67,7 @@ Tool | Description ## Cell Annotation & Feature Selection -Tools for marker gene identification and cell-type annotation +Tools for marker gene identification and cell-type annotation: Tool | Description --- | ---
Spatial2Galaxy