Computational Pathology Toolbox developed by TIA Centre, University of Warwick.
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Updated
Jun 14, 2024 - Python
Computational Pathology Toolbox developed by TIA Centre, University of Warwick.
Spatiotemporal modeling of spatial transcriptomics
A Hybrid CNN-Transformer Architecture for Precise Medical Image Segmentation
Cell tracking and segmentation software
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.
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.
Deep Learning Inferred Multiplex ImmunoFluorescence for IHC Image Quantification (https://deepliif.org) [Nature Machine Intelligence'22, CVPR'22, MICCAI'23, Histopathology'23, MICCAI'24]
StarDist - Object Detection with Star-convex Shapes
StarDist plugin for napari
Cell image analysis pipeline for RPE cell identification, counting and maturity classification
A style-aware deep learning model for adaptive cell instance segmentation by contrastive fine-tuning.
This repository is dedicated to the segmentation of histological features in regenerated vascular tissues obtained from tissue-engineered vascular grafts (TEVGs) implanted in sheep.
(NeurIPS 2022 CellSeg Challenge - 1st Winner) Open source code for "MEDIAR: Harmony of Data-Centric and Model-Centric for Multi-Modality Microscopy"
SuperDSM is a globally optimal segmentation method based on superadditivity and deformable shape models for cell nuclei in fluorescence microscopy images and beyond.
Official and maintained implementation of the dataset paper "An Instance Segmentation Dataset of Yeast Cells in Microstructures" [EMBC 2023].
A snakemake pipeline to perform cell segmentation on MERFISH spatial transcriptomics data.
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