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Welcome to the Zaritsky Lab GitHub

Motivated by fundamental questions in cell biology our lab produces biological insights along with specialized analytic tools that reveal hidden patterns in cell imaging data. This GitHub organization serves the purpose to store and maintain the products of our research.

  • Intracellular_Information_Processing - Spatiotemporal analysis of F-actin polymerization with micropillar arrays reveals synchronization between adhesion sites. This repo is under code review for clearance and maintainability.
  • shape-exp-modeling - Modeling the interplay between cell shape and expression in multiplexed imaging.
  • AnomalyDetectionScreening - Framework for hit identification in High Throughput Screening (HTS).
  • recurring-transient-communities - Detection of transient communities and hotspots in the developing Drosophila lymph gland, using ARCOS framework on Ca2+ readouts.
  • multiplexed-imaging-motifs-visualiser - Motif Visualizer for Multiplexed Imaging. A specialized tool designed to enhance the analysis and visualization of multiplexed imaging data.
  • muscle-formation-prediction - Machine learning inference of continuous single-cell state transitions during myoblast differentiation and fusion.
  • SLGC-tissue-similarity-and-grading - Nondestructive Spatial Lipidomics for Glioma Classification Tissue Similarity and Grading.
  • DISCOVER - Visual interpretability of image-based classification models by generative latent space disentanglement applied to in vitro fertilization.
  • MyocytesFusionSimulationsGeneratorAnalyzer - Myoblast fusion OOP implementations of fusion policies, and simulations analysis compared to experimental data.
  • IRM-Spreading-Dynamics - A custom pipeline for quantifying the spatiotemporal dynamics of platelet spreading process under IRM microscopy.
  • SpatiotemproalQuantificationMonolayerCellMigrationPipeline - A Matlab pipeline for spatiotemporal quantification of monolayer cell migration. The repository includes Matlab source code. This repository is part of the book series "Neubias Bioimage Analysis". The analysis pipeline includes segmentation, velocity measurements, kymographs and multi-dimensional representations and PCA of wound healing assays.
  • PropagationOfCellDeath - Ferroptosis occurs through an osmotic mechanism and propagates independently of cell rupture.

Please do all actions (open issues, file bug reports, file feature requests etc.) in the relevant repositories.

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  1. recurring-transient-communities recurring-transient-communities Public

    Detection of transient communities and hotspots in the developing Drosophila lymph gland, using ARCOS framework on Ca2+ readouts

    Python 1

  2. muscle-formation-prediction muscle-formation-prediction Public

    Machine learning inference of continuous single-cell state transitions during myoblast differentiation and fusion

    Jupyter Notebook 1 1

  3. DISCOVER DISCOVER Public

    Visual interpretability of image-based classification models by generative latent space disentanglement

    Jupyter Notebook 8

  4. AnomalyDetectionScreening AnomalyDetectionScreening Public

    Framework for hit identification in High Throughput Screening (HTS)

    Jupyter Notebook 1 1

  5. shape-exp-modeling shape-exp-modeling Public

    Jupyter Notebook

  6. Intracellular_Information_Processing Intracellular_Information_Processing Public

    Forked from Yishaiaz/Cell2CellComunicationAnalyzer

    Spatiotemporal analysis of F-actin polymerization with micropillar arrays reveals synchronization between adhesion sites

    Python 1 1

Repositories

Showing 10 of 14 repositories
  • SLGC-tissue-similarity-and-grading Public

    Nondestructive Spatial Lipidomics for Glioma Classification - Tissue Similarity and Grading

    zaritskylab/SLGC-tissue-similarity-and-grading’s past year of commit activity
    Python 1 GPL-3.0 1 0 0 Updated Nov 15, 2024
  • CELTIC Public

    CEll in silico Labeling using Tabular Input Context

    zaritskylab/CELTIC’s past year of commit activity
    0 0 0 0 Updated Nov 2, 2024
  • recurring-transient-communities Public

    Detection of transient communities and hotspots in the developing Drosophila lymph gland, using ARCOS framework on Ca2+ readouts

    zaritskylab/recurring-transient-communities’s past year of commit activity
    Python 1 0 0 0 Updated Nov 2, 2024
  • .github Public

    ✨special ✨ repository that you can use to add README.md to your public organization profile, visible to anyone.

    zaritskylab/.github’s past year of commit activity
    0 GPL-3.0 0 0 0 Updated Oct 28, 2024
  • Intracellular_Information_Processing Public Forked from Yishaiaz/Cell2CellComunicationAnalyzer

    Spatiotemporal analysis of F-actin polymerization with micropillar arrays reveals synchronization between adhesion sites

    zaritskylab/Intracellular_Information_Processing’s past year of commit activity
    Python 1 GPL-3.0 2 0 0 Updated Oct 28, 2024
  • IRM-Spreading-Dynamics Public

    A custom pipeline for quantifying the spatiotemporal dynamics of platelet spreading process under IRM microscopy.

    zaritskylab/IRM-Spreading-Dynamics’s past year of commit activity
    Python 1 LGPL-3.0 0 0 2 Updated Aug 30, 2024
  • DISCOVER Public

    Visual interpretability of image-based classification models by generative latent space disentanglement

    zaritskylab/DISCOVER’s past year of commit activity
    Jupyter Notebook 8 MIT 0 1 0 Updated Jul 4, 2024
  • zaritskylab/shape-exp-modeling’s past year of commit activity
    Jupyter Notebook 0 0 0 0 Updated Jun 2, 2024
  • AnomalyDetectionScreening Public

    Framework for hit identification in High Throughput Screening (HTS)

    zaritskylab/AnomalyDetectionScreening’s past year of commit activity
    Jupyter Notebook 1 MIT 1 0 0 Updated May 30, 2024
  • muscle-formation-prediction Public

    Machine learning inference of continuous single-cell state transitions during myoblast differentiation and fusion

    zaritskylab/muscle-formation-prediction’s past year of commit activity
    Jupyter Notebook 1 1 0 0 Updated Dec 27, 2023

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