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Single-cell fluorescence microscopy data analysis

• microscopy
• fluorescence-microscopy-imaging

PyTorch implementation of "TGSA: Protein-Protein Association-Based Twin Graph Neural Networks for Drug Response Prediction with Similarity Augmentation"

Data logistics system enabling real-time pathogen surveillance. Built for the Seattle Flu Study.

• postgres
• postgresql
• python
• infectious-disease

Official implementation of JAMIE, Joint variational Autoencoders for Multimodal Imputation and Embedding

• autoencoder
• imputation
• integration
• multimodal

A flexible Julia toolkit for high-dimensional cellular profiles

• julia
• morphological-analysis
• high-content-screening

scPair: Boosting single cell multimodal analysis by leveraging single cell atlases and implicit feature selection

DetecDiv provides a comprehensive set of tools to analyze time microscopy images using deep learning methods. The software structure is such that data can be processed either at the command line or using a graphical user-interface. Detecdiv classification models include : image classification and regression, semantic segmentation, LSTM networks to analyze data and image timeseries.

Analysis of cell migration in Igor Pro

• igor
• imagej
• cell-migration
• tracking

XitoSBML - the spatial SBML plugin for ImageJ

• sbml
• systems-biology
• spatial-sbml-plugin
• imagej

Python library for statistical analysis of mRNA and protein distributions in fluorescent microscopy images