Manuscript second round revisions

What's Changed

• Add updated DOI by @jenna-tomkinson in #73
• Compute qc counts per condition and overall by @jenna-tomkinson in #74

Full Changelog: v1.1...v1.2

Manuscript ready

In this release, all changes and analysis performed prepared the repository to be ready for manuscript after response to reviewers.

What's Changed

• Add minted DOI by @jenna-tomkinson in #53
• Process plate 6 by @jenna-tomkinson in #54
• Update plate 6 samples by @jenna-tomkinson in #55
• Fix Plate 6 metadata bug and rerun UMAP by @jenna-tomkinson in #58
• Fix UMAP NaN bug by @jenna-tomkinson in #59
• Apply single cell quality control by @jenna-tomkinson in #61
• Rerun umap embeddings with QC by @jenna-tomkinson in #62
• Rerun QC, update sc profiles, rerun UMAP embeddings by @jenna-tomkinson in #63
• Add single cell qc figures by @jenna-tomkinson in #64
• Add README updates by @jenna-tomkinson in #66
• Add plate 6 figshare doi by @jenna-tomkinson in #67
• Fix small qc issue by @jenna-tomkinson in #68
• Update licensing by @MattsonCam in #69
• Created CITATION.cff by @MattsonCam in #71
• Fixes for citation file error by @jenna-tomkinson in #72

Full Changelog: v1.0...v1.1

Release v1.0

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