Repository Index

ZetaStitcher is a tool designed to stitch large volumetric images such as those produced by Light-Sheet Fluorescence Microscopes.

• stitching
• microscopy
• microscopy-images
• fluorescence-microscopy-imaging

A framework for keeping biomedical text mining result up-to-date

• bionlp
• text-mining
• infrastructure
• python

Tool for segmentation in bioimaging

• napari
• bioimage-analysis

A foundation model-driven whole slide image-scale cell phenotyping method with QuPath integration Resources

• bioimage-analysis
• cell-classification
• computer-vision
• digital-pathology

3D shape analysis using deep learning

• cancer-biology
• cell-biology
• deep-learning
• geometric-deep-learning

A versatile single-cell cross-modality translation method via dual-aligned variational autoencoders

Simple dashboard to visualize trends in bloodwork biomarkers

Fast, deterministic cell-type deconvolution for million-bin spatial transcriptomics

• bioinformatics
• cell-type-deconvolution
• computational-biology
• deconvolution

An interactive image processing program for biologists written in Python.

• biologists
• python
• imagej
• calcium

Accurate segmentation of bacterial microscope images using deep learning synthetically generated image data.

• microscopy
• image-processing
• segmentation
• biology

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

A Python package to analyze matrix fiber orientation and intensity around cells as a proxy for cellular forces. Also measures alignment relative to X/Y axes, points and lines, with optional masks, a Python API and browser tools for analysis and group comparisons.

• contractility
• orientation
• fibrosis
• mechanobiology