Skip to content

big-fish 0.4
Compare
Choose a tag to compare
@Henley13 Henley13 released this 24 Sep 09:38
· 161 commits to master since this release
0.4
6d3eef9
This commit was created on GitHub.com and signed with GitHub’s verified signature. The key has expired.
GPG key ID: 4AEE18F83AFDEB23
Expired
Verified
Learn about vigilant mode.

Version 0.4:

Major upgrades
Add automated threshold setting for spot detection (69eaff1, f595466)
Add CI and unitary test coverage with travis and codecov (5989a92, 3dbaa77)
Major refactoring of subpackage bigfish.classification (09e9314, aba7778, 91a203e, eadcab1, 47539b4, e36c318, 94a7264, 433d2cb)
Move notebooks and examples data (c3de121, 253a1e6, 6848b70)

Minor upgrades
Add parameters to control the number spots and clusters in bigfish.detection.cluster_decomposition(61eea05, fe34a12)
Add contrast parameters in bigfish.plot (261bf36, 77f1f4c, 972cd7c)
Make I/O csv functions more flexible (e0f15a4)
Allow extra images and coordinates during results extraction in bigfish.stack.extract_cell (4d147ae)
Add cell_id in bigfish.stack.extract_cell outcome (7c13689)
Add functions to identify object detected in specific sub-cellular regions with bigfish.stack.identify_objects_in_region (542fe7a)
Refactor function bigfish.stack.remove_transcription_site to remove transcription sites (2480b3c)
Add function bigfish.stack.summarize_extraction_results to summarize extraction results in dataframe and csv (c97f55f, 553fadf)

Bug fixes
Fix bug in bigfish.segmentation.match_nuc_cell (5e06b3b)
Fix bug in bigfish.detection.build_reference_spot (def504a)
Remove possible duplicate coordinates for detected local maximum (490e050)
Fix bug with bigfish.detection.cluster_decomposition default results (d436dd4, 3d15094)
Fix dimension bug in bigfish.plot.plot_images (1e53812)
Fix potential bug in bigfish.stack.gaussian_filter for float images with values greater than 1 (6845dcd)
Fix bug in bigfish.detection.cluster_decomposition with negative background estimations (a3b4c1c)

Assets 2
Loading