Changelog

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.

[v0.4.1] - 2024-12-03

Changed

Always display trace ID, for every final (merged or singleton) spot. See Issue 18 and Issue 19.
Use implementation of NucleusNumber from gertils.

[v0.4.0] - 2024-11-27

This release supports looptrace v0.11.1.

Changed

Updated expected intra-field, inter-value delimiter to match changes in looptrace

[v0.3.2] - 2024-11-21

Changed

Update version of gertils dependency to latest version (v0.5.1).

[v0.3.1] - 2024-11-21

This is compatible with the 0.11.x line of looptrace.

Changed

Support Python 3.12.
Bump up dependencies on gertils and numpydoc_decorator.

[v0.3.0] - 2024-11-20

This is compatible with the 0.11.x line of looptrace.

Changed

Updated expected column and file names of input to match those emitted by looptrace processing; in particular, the file previously represented by *_rois.proximity_accepted.nuclei_labeled.csv is replaced by *_rois.with_trace_ids.csv.

Added

Now the joint tracing structure of ROIs from different regional barcodes / imaging timepoints can be visualised.

Changed

Adapted to new looptrace column names

[v0.2.0] - 2024-10-21

This is compatible with the 0.10.x line line of looptrace.

Changed

Patterns expected for input files:
- *_rois.merge_contributors.csv
- *_rois.proximity_rejected.csv
- *_rois.proximity_accepted.nuclei_labeled.csv
Visualising spots as discrete (nonoverlapping) sets
Visualising 5 sets of spots:
- Merge contributors
- Proximity rejects (spots too close together)
- Nuclear rejects (spots not in a nucleus)
- Accepted singletons
- Accepted mergers

[v0.1.0] - 2024-04-28

Added

This package, first release