Nellie: Automated organelle segmentation, tracking, and hierarchical feature extraction in 2D/3D live-cell microscopy
- biology
- fluorescence
- image-analysis
- image-processing
Repository Index
47,133 repositories indexed
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NeoDTI: Neural integration of neighbor information from a heterogeneous network for discovering new drug-target interactions
- computational-biology
- bioinformatics
- graph-convolution
- deep-learning
Machine learning for Analysis of Proteomics in Spatial biology - Nature Communications
- cell-annotation
- multiplexed-imaging
- mpif
A library to build and execute typed scientific workflows
MCP server for spatial transcriptomics analysis through natural language interfaces.
- bioinformatics
- cell-communication
- deconvolution
- machine-learning
3D shape analysis using deep learning
- cancer-biology
- cell-biology
- deep-learning
- geometric-deep-learning
Plugins for bone image analysis
- fiji-plugin
- image-analysis
- image-processing
- imagej-plugins
Fast, deterministic cell-type deconvolution for million-bin spatial transcriptomics
- bioinformatics
- cell-type-deconvolution
- computational-biology
- deconvolution
Z-stack Depth Colorcode ImageJ FIJI plugin
- imagej-plugin
- colorcode
- fiji
- imagej
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.
- imaging
- microscopy
- contractility
- collagen
Bioinformatics-themed kata for practicing string manipulation in a data transformation pipeline. Contains replit files to work quickly in an online dojo setting.
- kata
- challenge
- python
- bioinformatics
Simple webapp for generating small ligand conformers
- computational-biology
- computational-chemistry
- conformer-generation
- rdkit
XitoSBML - the spatial SBML plugin for ImageJ
- sbml
- systems-biology
- spatial-sbml-plugin
- imagej