v0.10.1

.github/workflows/main.yml

@@ -37,9 +37,9 @@ jobs:
       run: |
         pip install flake8
         # stop the build if there are Python syntax errors or undefined names
-        flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
+        flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics --exclude=tests,picasso/ext
         # exit-zero treats all errors as warnings. Line length and E203 match black configuration
-        flake8 . --count --exit-zero --max-complexity=10 --max-line-length=79 --extend-ignore=E203 --statistics
+        flake8 . --count --exit-zero --max-complexity=10 --max-line-length=79 --extend-ignore=E203 --statistics --exclude=tests,picasso/ext
     - name: Test with pytest
       run: |
         pip install pytest

changelog.md

@@ -1,6 +1,45 @@
 # Changelog
 
-Last change: 19-MAY-2026 CEST
+Last change: 28-MAY-2026 CEST
+
+## 0.10.1
+
+#### Localize
+- Fixed Gauss-fitting error when spot's sum is zero (zero division error)
+
+#### Render
+- Faster rendering through improvements for all blur methods and multi-level spatial indexing for quick zoomed-in rendering
+- Multichannel rendering supports colormaps, not only a single RGB color
+- Anisotripic DBSCAN (with faster implementation) [DOI: 10.1021/acs.jpcb.4c02030](https://doi.org/10.1021/acs.jpcb.4c02030)
+- Faster cluster centers calculation for SMLM clusterer, DBSCAN and HDBSCAN + `lpz` is saved if applicable
+- Load FOV keeps the aspect ratio of the input .txt file
+- Files dialog resizing fixed
+- Show 3D clustering widgets only when 3D data is loaded
+- Fixed linking saving `lpz`
+- Fixed high-resolution display of mask in Render (#666)
+- Removed render property cache since it did not provide any significant speed improvement
+
+#### SPINNA
+- Comparing models uses fitting modes (Bayesian, etc) and has a cleaner progress dialog
+- Convenient fitting of LE
+- Area/volume button removed (deduced automatically from densities and number of molecules in the exp. data)
+- Show 3D masking widgets only if 3D mask is selected
+- Batch analysis for LE fitting
+- Batch analysis does not require area input (if found in metadata)
+- Batch analysis has clear instructions on what columns are required via CLI and the docs update
+- Fixed NND plot reindexing after fitting (#665)
+
+#### Filter
+- Efficient Filter: much lower RAM usage + faster filtering by histogram selection (1D/2D), especially for very large datasets
+
+#### Others
+- Expanded the scope of the sample notebooks
+- Improved docstrings for 3D SMLM clusterer
+- Flake8 clean-up
+- Installers are distributed with readme.txt files (previously .rst)
+- Minor changes to documentation
+- Fixed subcluster check plot when one of the two populations is empty (#667)
+- Fixed 2D fitting with console printout and no multiprocessing
 
 ## 0.10.0
 

distribution/create_linux_shortcuts.py

@@ -4,7 +4,7 @@
 import os.path as op
 
 try:
-    import picasso
+    import picasso  # noqa: F401
 except ImportError:
     print(
         "This script must be run within an environment "
@@ -14,15 +14,29 @@
     raise
 
 SUBCMD = (
-    "average", "design", "filter", "localize", "render", "simulate", "spinna",
+    "average",
+    "design",
+    "filter",
+    "localize",
+    "render",
+    "simulate",
+    "spinna",
 )
 SCRIPT_PATH_ROOT = (os.sep, "usr", "bin", "picasso")
 DESKTOP_PATH_ROOT = (
-    os.sep, "usr", "share", "applications", "picasso_{subcmd}.desktop",
+    os.sep,
+    "usr",
+    "share",
+    "applications",
+    "picasso_{subcmd}.desktop",
 )
 SCRIPT_PATH_USER = ("~", "bin", "picasso")
 DESKTOP_PATH_USER = (
-    "~", ".local", "share", "applications", "picasso_{subcmd}.desktop",
+    "~",
+    ".local",
+    "share",
+    "applications",
+    "picasso_{subcmd}.desktop",
 )
 
 DESKTOP_TEMPLATE = """[Desktop Entry]

docs/files.rst

@@ -73,6 +73,6 @@ YAML Metadata Files
 YAML files are document-oriented text files that can be opened and changed with any text editor. In Picasso, YAML files are used to store metadata of movie or localization files.
 Each localization HDF5 file must always be accompanied with a YAML file of the same filename, except for the extension, which is ``.yaml``. **Deleting this YAML metadata file will result in failure of the Picasso software!**
 
-The metadata file must contain the keys: ``Width``, ``Height`` (size of the field of view in camera pixels), ``Frames`` (number of frames in the movie), and ``Pixelsize`` (camera pixel size in nm). Example files can be found `here <https://github.com/jungmannlab/picasso/tree/master/samples/data>`_
+The metadata file must contain the keys: ``Width``, ``Height`` (size of the field of view in camera pixels), ``Frames`` (number of frames in the movie), and ``Pixelsize`` (effective camera pixel size after magnification in nm). Example files can be found `here <https://github.com/jungmannlab/picasso/tree/master/samples/data>`_
 
 Raw binary files (i.e., with extension ``.raw``) may be accompanied by a YAML metadata file to store data about the movie dimensions, etc. While the metadata file, in this case, is not required, it reduces the effort of typing in this metadata each time the movie is loaded with ``Picasso: Localize``. To generate such a YAML metadata file, load the raw movie into ``Picasso: Localize``, then enter all required information in the appearing dialog. Check the checkbox ``Save info to yaml file`` and click ok. The movie will be loaded and the metadata saved in a YAML file. This file will be detected the next time this raw movie is loaded, and the metadata does not need to be entered again.

docs/render.rst

@@ -208,7 +208,7 @@ These columns can be used to plot density profiles of localizations along the re
 
 Save pick properties
 ^^^^^^^^^^^^^^^^^^^^
-Calculates the properties of each pick (i.e., mean frame, mean x mean y as well as kinetic information and saves it as an hdf5 file.
+Calculates the properties of each pick (i.e., mean frame, mean x mean y as well as kinetic information) and saves it as an hdf5 file.
 
 Save pick regions
 ^^^^^^^^^^^^^^^^^
@@ -272,7 +272,59 @@ Opens the Display Settings Dialog.
 
 Files (CTRL + F)
 ^^^^^^^^^^^^^^^^
-Open a dialog to select the color and toggle visibility for each loaded dataset.
+Opens the **Datasets** dialog, which lists every loaded channel and lets you
+control its title, visibility, color (or colormap), and relative intensity.
+A small horizontal gradient next to each channel previews what that channel
+will look like at intensity 0 → intensity 1.
+
+Each channel's *Color* dropdown is organised into three sections:
+
+* **Solid colors** — the 14 default named colors (``red``, ``cyan``,
+  ``green``, …). You can also type a hexadecimal code such as ``#FF5733``
+  directly into the dropdown. Solid colors are rendered as a black →
+  color ramp, exactly matching the previous "intensity × RGB" behaviour.
+* **Built-in colormaps** — one 3-stop *black → color → white* gradient
+  per default solid color, named ``<color>_gradient`` (e.g.
+  ``blue_gradient``, ``red_gradient``).
+* **Custom** — any user-defined colormaps (see "Edit custom colormaps…"
+  below). This section only appears once at least one custom colormap
+  has been defined.
+
+Channels are blended additively in the final image and clipped to 1.0,
+so overlapping high-intensity regions saturate toward the sum of the
+channel colors.
+
+The ``Automatic coloring`` checkbox overrides per-channel selections with
+HSV-spaced colors for as long as it's ticked. ``Save colors`` /
+``Load colors`` write / read a one-identifier-per-line ``.txt`` file —
+any name from the three dropdown sections (or a hex code) is valid.
+
+Edit custom colormaps
++++++++++++++++++++++
+Opens a small editor where you can create, rename, duplicate, or delete
+your own colormaps. Each custom colormap is a list of 2-5 *stops*; each
+stop has a position in [0, 1] and an RGB color. Stops are linearly
+interpolated into the 256-row look-up table (LUT) used at render time. Click any of the R / G / B cells to type a value, or **double-click** the row to pick the
+stop color from a standard color dialog. Use ``Add stop`` /
+``Remove stop`` to grow or shrink the gradient.
+
+Programmatic use
+++++++++++++++++
+The underlying conversion from solid colors or stops to a ``(256, 3)``
+LUT is also exposed as part of ``picasso.render``::
+
+    from picasso import render
+    lut_red   = render.solid_to_lut((1.0, 0.0, 0.0))     # black → red
+    lut_fire  = render.stops_to_lut([(0, 0, 0, 0),
+                                     (0.5, 1, 0, 0),
+                                     (1, 1, 1, 0)])      # black → red → yellow
+    qimage, *_ = render.render_scene(
+        locs=..., info=..., colors=[lut_red, lut_fire], ...
+    )
+
+Passing a list of LUTs to ``render_scene`` selects the per-channel
+colormap path; passing a list of plain RGB triplets (legacy) still works
+and is equivalent to ``solid_to_lut`` per channel.
 
 Left / Right / Up / Down
 ^^^^^^^^^^^^^^^^^^^^^^^^