All

22 repositories

DM4ISL
Public
Converting brightfield images into fluorescence imaged organelles using DDPM with averaging mechanism and hallucinations detection
Jupyter Notebook
•0•0•0•0•Updated Jun 11, 2026Jun 11, 2026
Interpretability
Public
Framework for quantifying confidence in in silico labeling predictions
Jupyter Notebook
•
Other
•0•0•0•0•Updated Jun 7, 2026Jun 7, 2026
recurring-transient-communities
Public
Detection of transient communities and hotspots in the developing Drosophila lymph gland, using ARCOS framework on Ca2+ readouts
Python
•
MIT License
•0•1•0•0•Updated Apr 10, 2026Apr 10, 2026
CISM
Public
A two-step method to identify local interconnected cell structures associated with a disease state in single cell spatial proteomics data
Jupyter Notebook
•
MIT License
•0•6•0•2•Updated Mar 16, 2026Mar 16, 2026
CellDeathSpreading
Public
CellDeathSpreading provides spatiotemporal metrics to detect locally propagative ferroptosis and relate collective death dynamics to mechanisms such as lysosome…
collective-behavior propagation cell-death
collective-behavior propagation cell-death apoptosis ferroptosis death-dynamics collective-death death-quantification
Jupyter Notebook
•
Other
•0•0•0•0•Updated Jan 16, 2026Jan 16, 2026
TNBC-SPATIAL-CHROMATIN-COMPACTION
Public
Spatially distinct chromatin compaction states predict neoadjuvant chemotherapy resistance in Triple Negative Breast Cancer
spatial-analysis chromatin gnn
spatial-analysis chromatin gnn xgboost-classifier fluorescence-lifetime tnbc
Jupyter Notebook
•
Other
•1•0•0•0•Updated Dec 21, 2025Dec 21, 2025
AnomalyDetectionScreening
Public
Framework for hit identification in High Throughput Screening (HTS)
Jupyter Notebook
•
Other
•1•1•2•0•Updated Sep 25, 2025Sep 25, 2025
shape-exp-modeling
Public
A framework for quantifying the relationship between cell shape and protein expression in multiplexed images. This relationship is assessed by measuring the cha…
Python
•
Other
•0•3•0•0•Updated Aug 3, 2025Aug 3, 2025
CELTIC
Public
CEll in silico Labeling using Tabular Input Context
image-to-image-translation in-silico-labeling label-free-microscopy
image-to-image-translation in-silico-labeling label-free-microscopy organelle-fluorescence-prediction cell-context-integration celtic-model out-of-distribution-data intracellular-organization deep-learning-in-cell-biology foundation-models-for-biology
Python
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Other
•2•1•0•0•Updated Jul 23, 2025Jul 23, 2025
.github
Public
✨special ✨ repository that you can use to add README.md to your public organization profile, visible to anyone.
GNU General Public License v3.0
•0•0•0•0•Updated Jun 22, 2025Jun 22, 2025
Nanoneedle-Lipidomics
Public
Nanoneedles Enable Spatiotemporal Lipidomics of Living Tissues
visualization processing machine-learning
visualization processing machine-learning statistics deep-learning cancer-research mass-spectrometry-imaging glioma
Python
•
GNU General Public License v3.0
•2•3•0•0•Updated Jun 20, 2025Jun 20, 2025
DISCOVER
Public
Visual interpretability of image-based classification models by generative latent space disentanglement
Jupyter Notebook
•
MIT License
•1•13•1•0•Updated Jun 16, 2025Jun 16, 2025
FANMODPlus
Public
FANMOD+ supporting the analysis of modern spatial multiplex single cell omics data
C
•0•4•2•0•Updated May 8, 2025May 8, 2025
metalspy
Public
Jupyter Notebook
•1•0•0•0•Updated Mar 24, 2025Mar 24, 2025
InSilicoLabeling
Public
Framework for in silico labeling project code infrastructure
GNU General Public License v3.0
•0•0•0•0•Updated Mar 5, 2025Mar 5, 2025
Intracellular_Information_Processing
Public
Spatiotemporal analysis of F-actin polymerization with micropillar arrays reveals synchronization between adhesion sites
Python
•
GNU General Public License v3.0
•2•1•0•0•Updated Oct 28, 2024Oct 28, 2024
IRM-Spreading-Dynamics
Public
A custom pipeline for quantifying the spatiotemporal dynamics of platelet spreading process under IRM microscopy.
dynamics microscopy irm
dynamics microscopy irm timelapse spatio-temporal-analysis
Python
•
GNU Lesser General Public License v3.0
•0•1•0•2•Updated Aug 30, 2024Aug 30, 2024
muscle-formation-prediction
Public
Machine learning inference of continuous single-cell state transitions during myoblast differentiation and fusion
Jupyter Notebook
•1•1•0•0•Updated Dec 27, 2023Dec 27, 2023
multiplexed-imaging-motifs-visualiser
Public
Motif Visualizer for Multiplexed Imaging
Python
•1•1•0•0•Updated Dec 3, 2023Dec 3, 2023
MyocytesFusionSimulationsGeneratorAnalyzer
Public
OOP implementations of fusion policies, and simulations analysis compared to experimental data
bootstrap synchronization simulation
bootstrap synchronization simulation oop fusion experimental-data
Python
•
GNU General Public License v3.0
•0•1•0•2•Updated Oct 3, 2023Oct 3, 2023
SpatiotemproalQuantificationMonolayerCellMigrationPipeline
Public
A Matlab pipeline for spatiotemporal quantification of monolayer cell migration. The repository includes Matlab source code. This repository is part of the book…
pca segmentation spatio-temporal-analysis
pca segmentation spatio-temporal-analysis cell-migration multidimensional-data bioimage-analysis kymography velocity-measurement
MATLAB
•
GNU General Public License v3.0
•0•1•0•0•Updated Mar 14, 2021Mar 14, 2021
PropagationOfCellDeath
Public
Ferroptosis occurs through an osmotic mechanism and propagates independently of cell rupture
propagation rupture cell-death
propagation rupture cell-death ferroptosis
Python
•2•2•0•0•Updated Apr 30, 2020Apr 30, 2020

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Zaritsky Lab

All

All

22 repositories

DM4ISL

Interpretability

recurring-transient-communities

CISM

CellDeathSpreading

TNBC-SPATIAL-CHROMATIN-COMPACTION

AnomalyDetectionScreening

shape-exp-modeling

CELTIC

.github

Nanoneedle-Lipidomics

DISCOVER

FANMODPlus

metalspy

InSilicoLabeling

Intracellular_Information_Processing

IRM-Spreading-Dynamics

muscle-formation-prediction

multiplexed-imaging-motifs-visualiser

MyocytesFusionSimulationsGeneratorAnalyzer

SpatiotemproalQuantificationMonolayerCellMigrationPipeline

PropagationOfCellDeath

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Repositories list

22 repositories