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    70 repositories

    • CPBS7601

      Public
      Course on computing skills in biomedical informatics
      Jupyter Notebook
      •
      BSD 3-Clause "New" or "Revised" License
      •4•0•0•0•Updated Nov 8, 2024Nov 8, 2024

    • coSMicQC

      Public
      Single cell Morphology Quality Control (coSMicQC)
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •2•6•28•0•Updated Nov 7, 2024Nov 7, 2024

    • CytoDataFrame

      Public
      An in-memory data analysis format for single-cell profiles alongside their corresponding images and segmentation masks.
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •1•0•3•0•Updated Nov 7, 2024Nov 7, 2024

    • sandbox

      Public
      A place to mess around learning github
      MIT License
      •22•0•0•2•Updated Nov 6, 2024Nov 6, 2024

    • Phenotypic_severity_and_variance

      Public
      Quantifying Zebrafish opercle bone morphology
      Jupyter Notebook
      •
      BSD 3-Clause "New" or "Revised" License
      •1•0•1•1•Updated Nov 4, 2024Nov 4, 2024

    • pediatric_cancer_atlas_profiling

      Public
      Image analysis and image-based profiling of pediatic cancer cell lines to extract morphological profiles.
      Jupyter Notebook
      •
      Creative Commons Zero v1.0 Universal
      •1•0•0•0•Updated Nov 1, 2024Nov 1, 2024

    • pyroptosis_signature_data_analysis

      Public
      Analysis repository for the pyroptosis morphology map
      Jupyter Notebook
      •
      BSD 3-Clause "New" or "Revised" License
      •1•2•15•2•Updated Nov 1, 2024Nov 1, 2024

    • nuclear_speckles_analysis

      Public
      Jupyter Notebook
      •
      Creative Commons Zero v1.0 Universal
      •1•0•1•1•Updated Nov 1, 2024Nov 1, 2024

    • pyroptosis_live-cell_timelapse

      Public
      BSD 3-Clause "New" or "Revised" License
      •1•0•0•0•Updated Nov 1, 2024Nov 1, 2024

    • GFF_organoid_image_profiling

      Public
      Jupyter Notebook
      •
      Creative Commons Zero v1.0 Universal
      •1•0•0•1•Updated Oct 30, 2024Oct 30, 2024

    • JUMP-single-cell

      Public
      Single cell analysis of the JUMP Cell Painting consortium pilot data (cpg0000)
      pythonimage-processingcellprofilerimage-analysiscell-paintingpycytominer
      Jupyter Notebook
      •
      BSD 3-Clause "New" or "Revised" License
      •5•4•1•1•Updated Oct 25, 2024Oct 25, 2024

    • demo-cellprofiler

      Public
      Demonstrating various CellProfiler development or implementations.
      Shell
      •
      BSD 3-Clause "New" or "Revised" License
      •1•0•1•0•Updated Oct 23, 2024Oct 23, 2024

    • CFReT-compound-prioritization-analysis

      Public
      Jupyter Notebook
      •1•1•0•0•Updated Oct 22, 2024Oct 22, 2024

    • targeted_fibrosis_drug_screen

      Public
      Image analysis and image-based profiling of a fibrosis drug screen to identify compound hits using a machine learning model.
      Jupyter Notebook
      •
      Creative Commons Zero v1.0 Universal
      •1•2•1•0•Updated Oct 16, 2024Oct 16, 2024

    • gene_dependency_representations

      Public
      Jupyter Notebook
      •
      BSD 3-Clause "New" or "Revised" License
      •5•2•0•1•Updated Oct 15, 2024Oct 15, 2024

    • live_cell_timelapse_apoptosis

      Public
      Jupyter Notebook
      •
      BSD 3-Clause "New" or "Revised" License
      •2•1•5•0•Updated Oct 11, 2024Oct 11, 2024

    • predicting-cell-injury-compounds

      Public
      Processing cell-injury profiles using Pycytominer to generate selected features profiles for training a multi-class regression model to identify cellular injury.
      Jupyter Notebook
      •
      Creative Commons Attribution 4.0 International
      •2•0•0•0•Updated Oct 11, 2024Oct 11, 2024

    • CP_Parallel

      Public
      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.
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •1•0•7•0•Updated Sep 23, 2024Sep 23, 2024

    • playbooks

      Public
      Playbooks relevant to the operations of the Way Lab and similar labs.
      Creative Commons Zero v1.0 Universal
      •1•0•1•0•Updated Sep 16, 2024Sep 16, 2024

    • phenotypic_profiling

      Public
      Machine learning for predicting 15 single-cell phenotypes from cell morphology profiles
      Jupyter Notebook
      •
      Creative Commons Attribution 4.0 International
      •3•2•0•0•Updated Sep 16, 2024Sep 16, 2024

    • NIH_Where2Submit

      Public
      This is a tool to help you figure out where to submit your grant in the NIH
      Jupyter Notebook
      •
      BSD 3-Clause "New" or "Revised" License
      •1•0•3•0•Updated Sep 9, 2024Sep 9, 2024

    • nf1_schwann_cell_morphology_signature

      Public
      This repository contains all the modules to split and train a binary classification model to predict NF1 null and wildtype genotype.
      Jupyter Notebook
      •
      Creative Commons Zero v1.0 Universal
      •2•0•3•0•Updated Sep 5, 2024Sep 5, 2024

    • Kan_we_predict_phenotypes

      Public
      A repo testing KANs on Image-based profiles
      Jupyter Notebook
      •2•0•1•0•Updated Sep 2, 2024Sep 2, 2024

    • nf1_schwann_cell_painting_data

      Public
      This repository contains all the modules to perform image-based analysis with CellProfiler on NF1 Schwann cell data.
      Jupyter Notebook
      •
      Creative Commons Zero v1.0 Universal
      •6•4•4•0•Updated Aug 20, 2024Aug 20, 2024

    • cellpainting_predicts_cardiac_fibrosis

      Public
      Image-based profiling and machine learning to predict failing vs. non-failing cardiac fibroblasts
      machine-learningimage-processingcellprofilercell-paintingimage-based-analysispycytominer
      Jupyter Notebook
      •
      Creative Commons Zero v1.0 Universal
      •4•4•1•0•Updated Aug 16, 2024Aug 16, 2024

    • MNIST_TD-VAE

      Public
      Temporal Difference Variational Auto-Encoder (TD-VAE) (Implementation in PyTorch)
      Python
      •27•0•0•0•Updated Aug 6, 2024Aug 6, 2024

    • nuclear_speckle_image_profiling

      Public
      Image analyis and image-based profiling of nuclear speckle dataset extracting intensity based features.
      Jupyter Notebook
      •
      Creative Commons Zero v1.0 Universal
      •1•0•0•0•Updated Aug 5, 2024Aug 5, 2024

    • live_cell_timelapse_apoptosis_analysis

      Public
      Jupyter Notebook
      •
      BSD 3-Clause "New" or "Revised" License
      •1•0•1•2•Updated Jul 31, 2024Jul 31, 2024

    • temporal_ViT

      Public
      This is the develpment of a temporal ViT using the MNIST dataset
      Jupyter Notebook
      •
      BSD 3-Clause "New" or "Revised" License
      •1•0•0•1•Updated Jul 24, 2024Jul 24, 2024

    • mitocheck_data

      Public
      All information regarding the download and processing of Mitocheck data from IDR study with accession idr0013 (screenA).
      Jupyter Notebook
      •
      Creative Commons Zero v1.0 Universal
      •5•2•5•0•Updated Jul 17, 2024Jul 17, 2024