Merge pull request #630 from jungmannlab/development

v0.9.9

Author: rafalkowalewski1

.bumpversion.cfg

@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 0.9.8
+current_version = 0.9.9
 commit = True
 tag = False
 parse = (?P<major>\d+)\.(?P<minor>\d+)\.(?P<patch>\d+)(\-(?P<release>[a-z]+)(?P<build>\d+))?

changelog.rst

@@ -3,8 +3,8 @@ Changelog
 
 Last change: 10-MAR-2026 CEST
 
-0.9.8
------
+0.9.8-9
+-------
 Small improvements:
 +++++++++++++++++++
 - Added a function ``picasso.lib.get_save_filename_ext_dialog`` that can also check for the existence of the files with other extenstions (for example, if the user tries to save a .yaml file with the same name as an existing .hdf5 file, it will ask if the user wants to overwrite the .hdf5 file). This is implemented in all GUI modules when saving files.
@@ -28,6 +28,7 @@ Small improvements:
 
 Bug fixes:
 ++++++++++
+- Fixed 3D multichannel rendering
 - Fixed Picasso Server launching in one-click-installers
 - Fixed 3D MLE fitting and cleaned the docstrings for better readability (``picasso.gaussmle``)
 - Fixed how Picasso: Simulates splits photons across binding events

distribution/picasso.iss

@@ -2,10 +2,10 @@
 AppName=Picasso
 AppPublisher=Jungmann Lab, Max Planck Institute of Biochemistry
 
-AppVersion=0.9.8
+AppVersion=0.9.9
 DefaultDirName={commonpf}\Picasso
 DefaultGroupName=Picasso
-OutputBaseFilename="Picasso-Windows-64bit-0.9.8"
+OutputBaseFilename="Picasso-Windows-64bit-0.9.9"
 ArchitecturesAllowed=x64
 ArchitecturesInstallIn64BitMode=x64
 

docs/conf.py

@@ -26,7 +26,7 @@
 # The short X.Y version
 version = ""
 # The full version, including alpha/beta/rc tags
-release = "0.9.8"
+release = "0.9.9"
 
 # -- General configuration ---------------------------------------------------
 

picasso/gui/rotation.py

@@ -744,13 +744,19 @@ def load_locs(self, update_window=False):
                 0
             ]  # only one pick, take the first element
             temp["z"] /= self.pixelsize
-            temp["z"] -= temp["z"].mean()
             # same for lpz if present
             if "lpz" in temp.columns:
                 temp["lpz"] /= self.pixelsize
             self.locs.append(temp)
             self.infos.append(self.window.window.view.infos[i])
 
+        # shift z positions of locs so that the middle of the dataset is
+        # at z = 0
+        all_locs_z = np.concatenate([_["z"].to_numpy() for _ in self.locs])
+        z_shift = all_locs_z.mean()
+        for i in range(n_channels):
+            self.locs[i]["z"] -= z_shift
+
         # assign self.group_color if single channel and group info
         # present
         if len(self.locs) == 1 and "group" in self.locs[0].columns:

picasso/version.py

@@ -1 +1 @@
-__version__ = "0.9.8"
+__version__ = "0.9.9"

pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "picassosr"
-version = "0.9.8"
+version = "0.9.9"
 authors = [
     {name = "Joerg Schnitzbauer", email = "joschnitzbauer@gmail.com"},
     {name = "Maximilian T. Strauss", email = "straussmaximilian@gmail.com"},

release/one_click_macos_gui/create_macos_dmg.sh

@@ -12,7 +12,7 @@ set -e  # Exit immediately on any error
 eval "$(conda shell.bash hook)"
 
 APP_NAME="Picasso"
-VERSION="0.9.8"
+VERSION="0.9.9"
 MAIN_BUNDLE_NAME="Picasso.app"
 DMG_NAME="Picasso-v$VERSION-macOS-Apple-Silicon"
 PYINSTALLER_FILE="../pyinstaller/picasso_pyinstaller.py"

release/one_click_windows_gui/create_installer_windows.bat

@@ -10,7 +10,7 @@ call conda activate picasso_installer
 call pip install build
 call python -m build
 
-call pip install "dist/picassosr-0.9.8-py3-none-any.whl"
+call pip install "dist/picassosr-0.9.9-py3-none-any.whl"
 call cd release/one_click_windows_gui
 
 call pip install pyinstaller==6.19.0

release/one_click_windows_gui/picasso_innoinstaller.iss

@@ -1,10 +1,10 @@
 [Setup]
 AppName=Picasso
 AppPublisher=Jungmann Lab, Max Planck Institute of Biochemistry
-AppVersion=0.9.8
+AppVersion=0.9.9
 DefaultDirName="C:\Picasso"
 DefaultGroupName=Picasso
-OutputBaseFilename="Picasso-Windows-64bit-0.9.8"
+OutputBaseFilename="Picasso-Windows-64bit-0.9.9"
 ArchitecturesAllowed=x64
 ArchitecturesInstallIn64BitMode=x64