v0.0.1

🚀 CellColoc v0.0.1

June 21, 2026

First public main release of CellColoc.

This initial release provides:

• the reusable cellcoloc Python package for interactive, segmentation-based colocalization analysis in microscopy images
• stepwise user-script workflows for VS Code interactive window and notebook-like execution
• OMIO-based microscopy loading with TZCYX handling
• automatic 2D versus 3D detection from the raw z dimension
• voxel-size resolution from explicit user input or OMIO metadata, with fallback to (1.0, 1.0, 1.0) when necessary
• channel-wise segmentation method selection with support for:
  • cellpose
  • otsu
  • li
  • percentile
• optional ROI drawing in napari
• optional whole-image analysis as one single ROI
• optional reuse of previously saved ROI masks
• per-cell overlap analysis and marker-positivity classification
• standardized detailed, summary, and overview result tables
• standardized export into a results/ subfolder next to the raw dataset
• occupancy metrics for every segmented channel
• optional third-channel segmentation and occupancy quantification
• optional third-channel cell-positivity analysis and double-positive reporting
• optional global z cropping for internal analysis
• optional global z projection using:
  • max
  • mean
  • median
  • std
  • var
• optional anisotropy handling for true 3D Cellpose runs
• optional flow3d_smooth support for Cellpose
• optional image prefiltering with:
  • gaussian
  • median
  • laplacian_of_gaussian
  • ordered prefilter chains
• optional label postfiltering with:
  • min_intensity
  • local_contrast
  • bright_pixel_support
  • ordered postfilter chains
• fast Cellpose cache-based refinement using stored network outputs
• optional manual napari mask editing followed by table recomputation
• reusable visualization helpers with selective layer refreshing in napari
• runtime fallback handling for cache and config directories when desktop libraries cannot write to default locations
• packaging metadata for installation via pip

Packaging notes:

• PyPI package name: cellcoloc
• import name: cellcoloc
• optional interactive extra: cellcoloc[interactive]
• optional tested Cellpose 3 extra: cellcoloc[cellpose3]