Release v1.0

Full release of image analysis, image-based profiling, and machine-learning pipelines to predict single-cell cardiac fibroblast phenotype (failing or non-failing).

What's Changed

• add modules and documentation by @jenna-tomkinson in #2
• add CellProfiler processing and edit IC module by @jenna-tomkinson in #4
• add module to CP and update notebook by @jenna-tomkinson in #5
• add normalization module by @jenna-tomkinson in #6
• add data from processing features by @jenna-tomkinson in #7
• rerun cfret plates and extract single cells by @jenna-tomkinson in #8
• Adding UMAP analysis by @gwaybio in #10
• Adding platemap visualization by @gwaybio in #12
• Adding linear modeling analysis by @gwaybio in #11
• Edit rerun cp and extract by @jenna-tomkinson in #16
• Refactor: rename folders, move+add metadata, edit README by @jenna-tomkinson in #17
• Refactor: change from PyBaSiC IC to CellProfiler IC by @jenna-tomkinson in #20
• Rerun CellProfiler analysis with all plates by @jenna-tomkinson in #21
• Adding plate 3 feature extraction processing by @axiomcura in #22
• added plate3 UMAPs by @axiomcura in #23
• Add new linear model figures by @jenna-tomkinson in #24
• Refactor Processing Data + Rerun UMAP Analysis for Plate 3 by @jenna-tomkinson in #26
• Update LM and UMAPs by @jenna-tomkinson in #27
• Add more single-cell images for UMAP figure by @jenna-tomkinson in #29
• Add nbconverted 2.find_sc notebook by @jenna-tomkinson in #30
• Plate 4 Image-based Analysis by @jenna-tomkinson in #31
• Plate 4 Analysis by @jenna-tomkinson in #32
• Add find_sc notebooks for LM and UMAP using Plate 4 data by @jenna-tomkinson in #33
• Add histogram plot and update LM by @jenna-tomkinson in #34
• Add quality control and rerun Plate 4 by @jenna-tomkinson in #36
• Machine learning model to predict failing or healthy cell type by @jenna-tomkinson in #37
• Extract and plot model coefficients by @jenna-tomkinson in #38
• Add rank plot using ML coefficients by @jenna-tomkinson in #39
• Update whole image and single cell QC to rerun model with improved dataset by @jenna-tomkinson in #40
• Rerun Plate 3 with QC and assess model generalizability by @jenna-tomkinson in #41
• Rerun QC for plates 1 and 2 and update analysis by @jenna-tomkinson in #42
• Update figures for manuscript by @jenna-tomkinson in #44
• Fix model bug, update QC, and rerun manuscript figures by @jenna-tomkinson in #45
• Add final updates by @jenna-tomkinson in #47

New Contributors

• @gwaybio made their first contribution in #10
• @axiomcura made their first contribution in #22

Full Changelog: https://github.com/WayScience/cellpainting_predicts_cardiac_fibrosis/commits/v1.0