Releases · WayScience/nf1_schwann_cell_painting_data

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