a generalist algorithm for cellular segmentation with human-in-the-loop capabilities
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Updated
May 26, 2024 - Jupyter Notebook
a generalist algorithm for cellular segmentation with human-in-the-loop capabilities
Source code for the paper "Cyto R-CNN and CytoNuke Dataset: Towards reliable whole-cell segmentation in bright-field histological images"
QuPath - Bioimage analysis & digital pathology
Segment Anything for Microscopy
Deep-Learning enabled quantitative image analysis of for the yeast full life cycle
Spatiotemporal modeling of spatial transcriptomics
Large-scale cell segmentation with cellpose.
Computational Pathology Toolbox developed by TIA Centre, University of Warwick.
Cell tracking and segmentation software
Deep Learning Inferred Multiplex ImmunoFluorescence for IHC Image Quantification (https://deepliif.org) [Nature Machine Intelligence'22, CVPR'22, MICCAI'23, Histopathology'23, MICCAI'24]
MIC-MAQ for Microscopy Images of Cells - Multi Analyses and Quantifications is an ImageJ/Fiji Plugin for automatic segmentation of nuclei and/or cells for quantifications in other channels including foci detection
Official implementation of "ASF-YOLO: A Novel YOLO Model with Attentional Scale Sequence Fusion for Cell Instance Segmentation".
Evaluation of label free cell and nuclei segmentation
ClusterMap for multi-scale clustering analysis of spatial gene expression
Interactive deep learning whole-cell segmentation and thresholding using partial annotations
Instance Segmentation with PyTorch & PyTorch Lightning.
StarDist - Object Detection with Star-convex Shapes
StarDist plugin for napari
Code repository for the conference paper "Organoid Segmentation Using Self-Supervised Learning: How Complex Should the Pretext Task Be?" published and presented at the International Conference on Biomedical and Bioinformatics Engineering (ICBBE) 2023.
Cell image analysis pipeline for RPE cell identification, counting and maturity classification
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