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Projects in Awesome Lists tagged with cell-segmentation

A curated list of projects in awesome lists tagged with cell-segmentation .

https://github.com/mouseland/cellpose

a generalist algorithm for cellular segmentation with human-in-the-loop capabilities

cell-biology cell-segmentation segmentation

Last synced: 13 May 2025

https://github.com/MouseLand/cellpose

a generalist algorithm for cellular segmentation with human-in-the-loop capabilities

cell-biology cell-segmentation segmentation

Last synced: 02 Apr 2025

https://github.com/stardist/stardist

StarDist - Object Detection with Star-convex Shapes

bioimage-analysis cell-segmentation deep-learning nuclei-segmentation object-detection python

Last synced: 21 Oct 2025

https://github.com/aristoteleo/spateo-release

Spatiotemporal modeling of spatial transcriptomics

3d-reconstruction cell-segmentation spatial-transcriptomics spatiotemporal

Last synced: 20 Feb 2026

https://github.com/oist/usiigaci

Usiigaci: stain-free cell tracking in phase contrast microscopy enabled by supervised machine learning

cell-biology cell-segmentation keras machine-learning mask-rcnn matplotlib python3 resnet-101 tensorflow tracking trackpy visualization

Last synced: 26 Jan 2026

https://github.com/nadeemlab/DeepLIIF

Deep Learning Inferred Multiplex ImmunoFluorescence for IHC Image Quantification (https://deepliif.org) [Nature Machine Intelligence'22, CVPR'22, MICCAI'23, Histopathology'23, MICCAI'24]

ai-ready cell-biology cell-segmentation cloud-native-applications datasets deep-learning digital-pathology image-segmentation immunohistochemical-images immunohistochemistry multiplex multitask-learning pathology pathology-gan pathology-image pytorch segmentation stitching super-resolution whole-slide-imaging

Last synced: 06 May 2025

https://github.com/royerlab/ultrack

Cell tracking and segmentation software

cell-segmentation cell-tracking cell-tracking-challenge gurobi

Last synced: 03 Jul 2025

https://github.com/ChristophReich1996/Cell-DETR

Official and maintained implementation of the paper "Attention-Based Transformers for Instance Segmentation of Cells in Microstructures" [BIBM 2020].

attention bibm-2020 cell-detr cell-segmentation deep-learning instance-segmentation synthetic-biology system-biology transformer

Last synced: 06 May 2025

https://github.com/marshuang80/cell-segmentation

PyTorch implementation of several neural network models for cellular image segmentation

cell-segmentation pytorch segmentation unet

Last synced: 12 Apr 2025

https://github.com/joda01/imagec

imageC / EVAnalyzer2 - High throughput biological image processor

bioimage-analysis bioimage-informatics biology cell-segmentation evanalyzer image-processing opencv science

Last synced: 01 Feb 2026

https://shjo-april.github.io/Chain-of-Prompts/

[MICCAI 2026 Early Accept] Chain-of-Prompts (CoP): One Click per Cell Type Suffices, Training-free Group Interaction for Cell Instance Segmentation

cell cell-segmentation chain-of-prompts group-prompting histopathology instance-segmentation interactive-segmentation medical-imaging miccai2026 segment-anything training-free

Last synced: 25 Jun 2026

https://github.com/tzmcion/cell-morphology

An app for segmentation and classification of images of cells from optical microscope. This project uses marker controlled watershed (openCv), and pretrained ResNet-50 model (tensorflow)

cell-classification cell-segmentation optical-microscope-classification optical-microscope-segmentation resnet50-classification watershed-algorithm

Last synced: 18 Jan 2026

https://github.com/adamjstewart/cell_segmentation

:microscope: A U-Net based deep learning architecture for cell segmentation

cell-segmentation deep-learning pytorch u-net

Last synced: 19 Apr 2026

https://github.com/cellsepi/cellsepi

Segmentation of microscopy images and data analysis pipeline with a graphical user interface, powered by Cellpose.

biology cell-biology cell-segmentation cellpose cellpose-segmentation cellsegmentation segmentation

Last synced: 17 Jun 2026

https://github.com/kostrykin/rfove

Region-based Fitting of Overlapping Ellipses (original implementation by C. Panagiotakis and A.A. Argyros, Image Vis Comput 2020)

cell-counting cell-detection cell-segmentation image-segmentation instance-segmentation object-detection object-segmentation

Last synced: 01 Nov 2025

https://github.com/turhancan97/cell_size

Batch cell segmentation and size estimation for microscopy images using Cellpose-SAM, with automated good/bad cell classification and an interactive Gradio demo.

biology cell-segmentation cell-size cellpose computer-vision deep-learning gradio hydra image-segmentation microscopy-image-analysis pytorch

Last synced: 21 Jun 2026

https://github.com/unikill066/xenium_cell_segmentation

End-to-end pipeline for spinal-cord microscopy segmentation with Cellpose, tiling, and mask stitching.

cell-segmentation cellpose cellpose-segmentation xenium

Last synced: 22 Jun 2025

https://github.com/viacheslavdanilov/histology_segmentation

This repository is dedicated to the segmentation of histological features in regenerated vascular tissues obtained from tissue-engineered vascular grafts (TEVGs) implanted in sheep.

cell-segmentation deep-learning digital-pathology histological-features semantic-segmentation vascular-tissue-engineering

Last synced: 20 Jun 2026

https://github.com/royerlab/ultrack-atini-2025

Ultrack's hands-on exercise for Advanced Techniques in NeuroImaging (ATiNI) 2025

cell-segmentation cell-tracking cell-tracking-challenge

Last synced: 03 Feb 2026

https://github.com/wehi-soda-hub/spatialvpt

Segmentation and QC workflow for MERSCOPE using vizgen-postprocessing tool

cell-segmentation merscope qc

Last synced: 16 Jan 2026