All notable changes to this project will be documented in this file.
The format is based on Keep a Changelog, and this project adheres to Semantic Versioning.
- Iniatialization of this CHANGELOG file to track changes as the version increments
- Fixed bug in sum signal
- Exposed tolerance parameter in the adaptive filter barcodes method
- Added plot for scale factor magnitude vs bit index
- Fixed barcode partitioning to include cells from adjacent fields of view when a cell falls across fov boundaries
- Addressed bugs present in cleaning overlapping cells and assigning them to a fov
- Added option to draw field of view labels overlaid on the mosaic
- Added task to evaluate whether a parallel analysis task has completed
- Changed the clean overlapping cells to run in parallel
- Snakemake job inputs were simplified using the ParallelCompleteTask to improve DAG construction speed and overall snakemake runtime performance
- Updated the filemap to only store the file name so that it can easily be pointed to new data home directories. This change maintains backward compatibility.
- Improved decoding speed
- Parameters to filter tasks that enable removing barcodes that were putatively duplicated across adjacent z planes.
- Fixed bug and edge cases in removal of barcodes duplicated across z planes. Moved to the decode step to prevent unintended conflict with misidentification rate determination.
- An alternative Lucy-Richardson deconvolution approach that requires ~10x fewer iterations.