a generalist algorithm for cellular segmentation with human-in-the-loop capabilities
- segmentation
- cell-segmentation
- cell-biology
Repository Index
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- foundation-model
- gpt
- single-cell
StarDist - Object Detection with Star-convex Shapes
- bioimage-analysis
- cell-segmentation
- nuclei-segmentation
- object-detection
Segment Anything for Microscopy
- microscopy-images
- segment-anything
- segmentation
- cell-segmentation
Deep Learning Library for Single Cell Analysis
- deep-learning
- tensorflow
- instance-segmentation
- cell-biology
CellViT: Vision Transformers for Precise Cell Segmentation and Classification
- ai
- cell
- digitalpathology
- microscopy
Using deep stacked residual bidirectional LSTM cells (RNN) with TensorFlow, we do Human Activity Recognition (HAR). Classifying the type of movement amongst 6 categories or 18 categories on 2 different datasets.
- tensorflow
- lstm
- rnn
- stacked-layers
Codebase for "A Foundation Model for Cell Segmentation"
Usiigaci: stain-free cell tracking in phase contrast microscopy enabled by supervised machine learning
- tensorflow
- python3
- keras
- resnet-101
Open-source software for exploring and analyzing large, high-dimensional image-derived data.
- cellprofiler-analyst
- cellprofiler
- image-analysis
- machine-learning
🏃 The go-to single-cell Foundation Model
- batch-correction
- cell-biology
- celltype-annotation
- denoising
A tool for cell instance aware segmentation in densely packed 3D volumetric images
- segmentation
- deep-learning
- bioinformatics
- neural-network
Learning cell communication from spatial graphs of cells
- tensorflow
- gnn
- glm
- cvae
A curated list of awesome cytodata resources https://www.cytodata.org/awesome-cytodata/
- awesome-list
- awesome
- image-analysis
- morphology
Nellie: Automated organelle segmentation, tracking, and hierarchical feature extraction in 2D/3D live-cell microscopy
- biology
- fluorescence
- image-analysis
- image-processing
PyTorch implementation of the MIDAS algorithm for single-cell multimodal data integration (Nature Biotechnology 2024).
- deep-generative-model
- deep-learning
- single-cell-data-integration
- single-cell-multiomics
Machine learning for Analysis of Proteomics in Spatial biology - Nature Communications
- cell-annotation
- multiplexed-imaging
- mpif
Deep learning model for single-cell inference of multi-omic profiles from a single input modality.
- single-cell
- scrna-seq
- scatac-seq
- deep-neural-networks
MCP server for spatial transcriptomics analysis through natural language interfaces.
- bioinformatics
- cell-communication
- deconvolution
- machine-learning
A foundation model-driven whole slide image-scale cell phenotyping method with QuPath integration Resources
- bioimage-analysis
- cell-classification
- computer-vision
- digital-pathology
Deciphering cell-cell communication from spatially resolved transcriptomic data at single-cell resolution with subgraph-based attentional graph neural network
3D shape analysis using deep learning
- cancer-biology
- cell-biology
- deep-learning
- geometric-deep-learning
An interactive tool for segmenting yeast cells using deep learning.
Interpretable drug response prediction with graph neural networks over drugs, cell lines, and genes.