Full release of image analysis and image-based profiling pipelines to extract and format single-cell morphological profiles from Schwann cells with wildtype and null NF1 genotypes.
What's Changed
- add main README and download data by @jenna-tomkinson in #2
- Create IC module by @jenna-tomkinson in #3
- CellProfiler analysis module by @jenna-tomkinson in #5
- Add Plate 3 and run IC pipeline by @jenna-tomkinson in #7
- add plate 3 analysis without run by @jenna-tomkinson in #9
- Run plates 3 and 3prime by @jenna-tomkinson in #10
- Correct metadata for plate 3 and rerun processing features by @jenna-tomkinson in #11
- Fix plates 1 and 2 IC + rerun by @jenna-tomkinson in #14
- Add Cameron's suggestions from PR #14 by @jenna-tomkinson in #15
- Add Plate 4 Images by @jenna-tomkinson in #16
- Analyze Plate 4 and rerun analysis + IC with CellProfiler Parallel by @jenna-tomkinson in #17
- Process CellProfiler Extracted Features by @jenna-tomkinson in #19
- Rerun analysis with Zernike features by @jenna-tomkinson in #20
- Add bulk profiles for each plate by @jenna-tomkinson in #21
- Barcode Update With Plate3_prime and Naming by @axiomcura in #24
- Update pycytominer pipelines by @gwaybio in #23
- Fix main environment by @jenna-tomkinson in #25
- Linear Model Coefficient Analysis by @jenna-tomkinson in #26
- Fix Issue in Main README by @jenna-tomkinson in #27
- Add UMAP module by @jenna-tomkinson in #29
- Image-based Profiling of Plate 5 by @jenna-tomkinson in #31
- Develop Whole Image Quality Control and Rerun Plate 5 by @jenna-tomkinson in #33
- Rerun plates 3, 3 prime, and 4 with QC by @jenna-tomkinson in #34
- Fix CytoTable Bug by @jenna-tomkinson in #35
- Update LM and UMAPs by @jenna-tomkinson in #37
- Normalize plate 4 with cells not treated with construct by @MattsonCam in #39
- Add UMAP with concat normalized data from plates 5, 3, and 3 prime by @jenna-tomkinson in #38
- Add linear model results from concat plates by @jenna-tomkinson in #40
- Normaize Plate 4 with respect to Null Cells by @MattsonCam in #41
- Add concat plate LM visualizations by @jenna-tomkinson in #42
- Remove HET cells from plates 3 and 3 prime by @jenna-tomkinson in #43
- Update Plate 4 normalization to standardize to both WT and Null controls by @jenna-tomkinson in #44
- Add updated plate 5 processed files and UMAPs by @jenna-tomkinson in #46
- Fix bug due to location metadata by @jenna-tomkinson in #47
- Fix Plate_3_prime metadata plate column bug in CellProfiler by @jenna-tomkinson in #48
- Update concat plate UMAP embeddings by @jenna-tomkinson in #49
- Add img quality data to use in manuscript by @jenna-tomkinson in #51
- Software garden and add figshare DOIs by @jenna-tomkinson in #52
New Contributors
- @axiomcura made their first contribution in #24
- @gwaybio made their first contribution in #23
- @MattsonCam made their first contribution in #39
Full Changelog: https://github.com/WayScience/nf1_cellpainting_data/commits/v1.0
Contributors
gwaybio, axiomcura, and 2 other contributors