The Way Lab's repositories
cellpainting_predicts_cardiac_fibrosis
Image-based profiling and machine learning to predict failing vs. non-failing cardiac fibroblasts
JUMP-single-cell
Single cell analysis of the JUMP Cell Painting consortium pilot data (cpg0000)
nf1_schwann_cell_painting_data
This repository contains all the modules to perform image-based analysis with CellProfiler on NF1 Schwann cell data.
waysciencelab.com
Homepage for all happenings in the Way Lab at CU Anschutz
mitocheck_data
All information regarding the download and processing of Mitocheck data from IDR study with accession idr0013 (screenA).
phenotypic_profiling
Machine learning for predicting 15 single-cell phenotypes from cell morphology profiles
pyroptosis_signature_data_analysis
Analysis repository for the pyroptosis morphology map
pyroptosis_signature_image_profiling
This repository contains the pipelines used to analyze the data sets from the Interstellar collaboration.
targeted_fibrosis_drug_screen
Image analysis and image-based profiling of a fibrosis drug screen to identify compound hits using a machine learning model.
nf1_schwann_cell_morphology_signature
This repository contains all the modules to split and train a binary classification model to predict NF1 null and wildtype genotype.
CP_Parallel
Traditionally, headless mode for CellProfiler can only run with one worker at a time with one set of images, which can take a long time sequentially. CP Parallel will run multiple instances of CellProfiler in parallel across plates.
Cytotoxic-Nuisance-Metadata-Analysis
Processing cell-injury profiles using Pycytominer to generate selected features profiles for training a multi-class regression model to identify cellular injury.
CytoTrajectory
CytoTrajectory: Drug Screening Trajectory Tracking with Image-based Profile Interpretability using Variational Auto Encoders (VAEs)
gc-bucket-alsf-predicting-nuclear-speckles
GCP bucket for ALSF collaborations on predicting nuclear speckles.
Kan_we_predict_phenotypes
A repo testing KANs on Image-based profiles
MNIST_TD-VAE
Temporal Difference Variational Auto-Encoder (TD-VAE) (Implementation in PyTorch)
NIH_Where2Submit
This is a tool to help you figure out where to submit your grant in the NIH
nuclear_speckle_image_profiling
Image analyis and image-based profiling of nuclear speckle dataset extracting intensity based features.
Phenotypic_severity_and_variance
Quantifying Zebrafish opercle bone morphology
playbooks
Playbooks relevant to the operations of the Way Lab and similar labs.
sandbox
A place to mess around learning github
temporal_ViT
This is the develpment of a temporal ViT using the MNIST dataset