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The Top 23 Cell Segmentation Open Source Projects

Open source projects categorized as Cell Segmentation
Categories > Cell Segmentation
Cellpose ⭐ 1,198
a generalist algorithm for cellular segmentation with human-in-the-loop capabilities
dependent packages 29total releases 66most recent commit 23 days agopypi cellpose} Downloads
Qupath ⭐ 934
QuPath - Bioimage analysis & digital pathology
most recent commit 4 months ago
Stardist ⭐ 788
StarDist - Object Detection with Star-convex Shapes
dependent packages 22total releases 29most recent commit 4 months agopypi stardist} Downloads
Tiatoolbox ⭐ 277
Computational Pathology Toolbox developed by TIA Centre, University of Warwick.
dependent packages 1total releases 23most recent commit 4 months agopypi tiatoolbox} Downloads
Micro Sam ⭐ 240
Segment Anything for Microscopy
most recent commit 4 months ago
Usiigaci ⭐ 187
Usiigaci: stain-free cell tracking in phase contrast microscopy enabled by supervised machine learning
most recent commit 4 years ago
Etl_unicorn ⭐ 156
数据可视化, 数据挖掘, 数据处理 ETL
most recent commit 2 years ago
Spateo Release ⭐ 135
Spatiotemporal modeling of spatial transcriptomics
total releases 3most recent commit 5 months ago
Deepliif ⭐ 126
Deep Learning Inferred Multiplex ImmunoFluorescence for IHC Image Quantification (https://deepliif.org) [Nature Machine Intelligence'22, CVPR'22, MICCAI'23, Histopathology'23]
total releases 6most recent commit 4 months ago
Celldetection ⭐ 93
Instance Segmentation with PyTorch & PyTorch Lightning.
most recent commit 4 months ago
Hiformer ⭐ 86
HiFormer: Hierarchical Multi-scale Representations Using Transformers for Medical Image Segmentation (WACV 2023)
most recent commit 7 months ago
Mediar ⭐ 83
(NeurIPS 2022 CellSeg Challenge - 1st Winner) Open source code for "MEDIAR: Harmony of Data-Centric and Model-Centric for Multi-Modality Microscopy"
most recent commit 6 months ago
Cell Detr ⭐ 57
Official and maintained implementation of the paper "Attention-Based Transformers for Instance Segmentation of Cells in Microstructures" [BIBM 2020].
most recent commit 2 years ago
Ultrack ⭐ 53
Cell tracking and segmentation software
most recent commit 5 months ago
Cellseg_models.pytorch ⭐ 40
Encoder-Decoder Cell and Nuclei segmentation models
total releases 22most recent commit 8 months ago
Impartial ⭐ 28
Interactive deep learning whole-cell segmentation and thresholding using partial annotations
most recent commit 7 months ago
Cell Segmentation ⭐ 26
PyTorch implementation of several neural network models for cellular image segmentation
most recent commit 5 years ago
Simpli ⭐ 24
SIMPLI is a highly configurable pipeline for the analysis of multiplexed imaging data.
most recent commit a year ago
Cell_segmentation_and_tracking ⭐ 20
For cell segmentation and tracking.
most recent commit 4 years ago
Clustermap ⭐ 18
ClusterMap for multi-scale clustering analysis of spatial gene expression
most recent commit 2 years ago
Cell Segmentation ⭐ 14
Automated identification of cell boundaries from the pathological video data
most recent commit 6 years ago
Csml ⭐ 9
Cell Segmenter using Machine Learning
most recent commit 10 months ago
Yeast In Microstructures Dataset ⭐ 8
Official and maintained implementation of the dataset paper "An Instance Segmentation Dataset of Yeast Cells in Microstructures" [EMBC 2023].
most recent commit 9 months ago
The 3 Most Depended On Cell Segmentation Open Source Projects
Cellpose ⭐ 1,198
a generalist algorithm for cellular segmentation with human-in-the-loop capabilities
dependent packages 29total releases 66latest release August 25, 2023most recent commit 23 days agopypi cellpose} Downloads
Stardist ⭐ 788
StarDist - Object Detection with Star-convex Shapes
dependent packages 22total releases 29latest release July 21, 2023most recent commit 4 months agopypi stardist} Downloads
Tiatoolbox ⭐ 277
Computational Pathology Toolbox developed by TIA Centre, University of Warwick.
dependent packages 1total releases 23latest release July 25, 2023most recent commit 4 months agopypi tiatoolbox} Downloads
The 8 Latest Releases In Cell Segmentation Open Source Projects
Cellpose ⭐ 1,198
a generalist algorithm for cellular segmentation with human-in-the-loop capabilities
dependent packages 29total releases 66latest release August 25, 2023most recent commit 23 days agopypi cellpose} Downloads
Epitools ⭐ 6
Quantifying 2D cell shape and epithelial tissue dynamics
total releases 12latest release August 15, 2023most recent commit 9 months ago
Tiatoolbox ⭐ 277
Computational Pathology Toolbox developed by TIA Centre, University of Warwick.
dependent packages 1total releases 23latest release July 25, 2023most recent commit 4 months agopypi tiatoolbox} Downloads
Stardist ⭐ 788
StarDist - Object Detection with Star-convex Shapes
dependent packages 22total releases 29latest release July 21, 2023most recent commit 4 months agopypi stardist} Downloads
Cellseg_models.pytorch ⭐ 40
Encoder-Decoder Cell and Nuclei segmentation models
total releases 22latest release July 10, 2023most recent commit 8 months ago
Spateo Release ⭐ 135
Spatiotemporal modeling of spatial transcriptomics
total releases 3latest release December 15, 2022most recent commit 5 months ago
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