Changelog#

Version 0.2.8#

  • Major refactoring of ``spatial_cell`` function: * Refactored to use GeoDataFrame.plot() for efficient rendering and automatic legend generation * Integrated scanpy-style background image processing with scale_factor support * Fixed coordinate alignment issue when plotting subset data (image extent now matches data range) * Added support for gene expression visualization (color parameter can be a gene name from adata.var_names) * Legend and colorbar now positioned outside the plot area (right side) similar to sc.pl.spatial * Added xlabel, ylabel, and show_ticks parameters for axis customization * library_id parameter now auto-selects first available library_id when not specified (similar to sc.pl.spatial) * Added alpha_img parameter to control background image transparency * Improved categorical legend generation with custom palette support

  • Enhanced ``read_hd_cellseg`` function: * Added automatic detection of alternative segmentation file names (e.g., cell_segmentations.geojson) * Automatically adds spot_diameter_fullres to scalefactors if missing (required for sc.pl.spatial compatibility) * Improved error messages with suggestions for alternative filenames

  • Documentation improvements: * Reorganized usage documentation into separate files (reading.rst, visualization.rst, computing_distances.rst) * Added directory structure requirements to reading documentation * Added comprehensive visualization optimization guide for large datasets * Updated examples with gene expression visualization

Version 0.2.5#

  • Fixed read_hd_cellseg bug where cellid column was lost after reset_index()

  • Added robust handling for cases where reset_index() creates 'index' column instead of 'cellid'

  • Improved error messages for better debugging

Version 0.2.4#

  • Fixed read_hd_cellseg bug where cellid column was missing when creating GeoDataFrame

  • Added field name detection for cell_id column (supports multiple naming variants)

Version 0.2.3#

  • Fixed read_hd_cellseg to properly store cell geometries in GeoDataFrame format

Version 0.2.2#

  • Added spatial_cell plotting function for visualizing cells as polygons

  • Modified read_hd_cellseg to store cell geometries in both GeoDataFrame and WKT format

  • Renamed trackcell/io/spatial.py to trackcell/io/read_data.py

  • Renamed trackcell/pl/spatial.py to trackcell/pl/plot.py

  • Improved documentation and examples

Version 0.2.1#

  • Added read_hd_bin function for reading bin-level data (2um/8um/16um)

  • Enhanced hd_labeldist with automatic coordinate resolution detection

  • Improved memory efficiency with cKDTree method

Version 0.2.0#

  • Initial release with core functionality

  • read_hd_cellseg for reading cell segmentation data

  • hd_labeldist for computing distances to labels