Spatiotemporal modeling of spatial transcriptomics
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Updated
Jun 3, 2024 - Python
Spatiotemporal modeling of spatial transcriptomics
Computational Pathology Toolbox developed by TIA Centre, University of Warwick.
a generalist algorithm for cellular segmentation with human-in-the-loop capabilities
A Hybrid CNN-Transformer Architecture for Precise Medical Image Segmentation
Cell tracking and segmentation software
QuPath - Bioimage analysis & digital pathology
Official implementation of "ASF-YOLO: A Novel YOLO Model with Attentional Scale Sequence Fusion for Cell Instance Segmentation".
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.
Deep-Learning enabled quantitative image analysis of for the yeast full life cycle
Instance Segmentation with PyTorch & PyTorch Lightning.
Segment Anything for Microscopy
Source code for the paper "Cyto R-CNN and CytoNuke Dataset: Towards reliable whole-cell segmentation in bright-field histological images"
Large-scale cell segmentation with cellpose.
Interactive deep learning whole-cell segmentation and thresholding using partial annotations
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
Evaluation of label free cell and nuclei segmentation
ClusterMap for multi-scale clustering analysis of spatial gene expression
StarDist - Object Detection with Star-convex Shapes
StarDist plugin for napari
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