aristoteleo/spateo-release

Spatiotemporal modeling of spatial transcriptomics

Language: Python - Size: 33.1 MB - Last synced: 5 days ago - Pushed: 5 days ago - Stars: 146 - Forks: 23

MouseLand/cellpose

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

Language: Jupyter Notebook - Size: 108 MB - Last synced: 6 days ago - Pushed: 6 days ago - Stars: 1,204 - Forks: 349

stardist/stardist

StarDist - Object Detection with Star-convex Shapes

Language: Python - Size: 118 MB - Last synced: 4 days ago - Pushed: about 1 month ago - Stars: 825 - Forks: 213

computational-cell-analytics/micro-sam

Segment Anything for Microscopy

Language: Jupyter Notebook - Size: 39 MB - Last synced: 5 days ago - Pushed: 5 days ago - Stars: 301 - Forks: 35

cellimnet/scellseg-publish

A style-aware deep learning model for adaptive cell instance segmentation by contrastive fine-tuning.

Language: Python - Size: 253 MB - Last synced: 9 days ago - Pushed: about 1 month ago - Stars: 10 - Forks: 2

AllenNeuralDynamics/aind-large-scale-cellpose

Large-scale cell segmentation with cellpose.

Language: Python - Size: 92.8 KB - Last synced: 9 days ago - Pushed: 10 days ago - Stars: 0 - Forks: 0

TissueImageAnalytics/tiatoolbox

Computational Pathology Toolbox developed by TIA Centre, University of Warwick.

Language: Python - Size: 524 MB - Last synced: 5 days ago - Pushed: 10 days ago - Stars: 327 - Forks: 71

royerlab/ultrack

Cell tracking and segmentation software

Language: Python - Size: 75.9 MB - Last synced: 10 days ago - Pushed: 11 days ago - Stars: 62 - Forks: 6

okunator/cellseg_models.pytorch

Encoder-Decoder Cell and Nuclei segmentation models

Language: Python - Size: 68.2 MB - Last synced: 10 days ago - Pushed: 7 months ago - Stars: 63 - Forks: 3

MultimodalImagingCenter/MIC-MAQ

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

Language: Java - Size: 12.6 MB - Last synced: 12 days ago - Pushed: 12 days ago - Stars: 0 - Forks: 0

mkang315/ASF-YOLO

Official implementation of "ASF-YOLO: A Novel YOLO Model with Attentional Scale Sequence Fusion for Cell Instance Segmentation".

Language: Python - Size: 253 MB - Last synced: 13 days ago - Pushed: 13 days ago - Stars: 46 - Forks: 2

lstrgar/SEG

Evaluation of label free cell and nuclei segmentation

Language: Jupyter Notebook - Size: 19.1 MB - Last synced: 14 days ago - Pushed: 14 days ago - Stars: 6 - Forks: 3

berkyalcinkaya/yeastvision

Deep-Learning enabled quantitative image analysis of for the yeast full life cycle

Language: Python - Size: 178 MB - Last synced: 14 days ago - Pushed: 15 days ago - Stars: 2 - Forks: 2

nadeemlab/ImPartial

Interactive deep learning whole-cell segmentation and thresholding using partial annotations

Language: Jupyter Notebook - Size: 154 MB - Last synced: 10 days ago - Pushed: 12 days ago - Stars: 29 - Forks: 3

FZJ-INM1-BDA/celldetection

Instance Segmentation with PyTorch & PyTorch Lightning.

Language: Python - Size: 15.3 MB - Last synced: 25 days ago - Pushed: 25 days ago - Stars: 112 - Forks: 21

Curovearth/Cell-Segmentation

Cell segmentation performed as part of Digital Image Processing course.

Language: Jupyter Notebook - Size: 64.6 MB - Last synced: 26 days ago - Pushed: over 1 year ago - Stars: 0 - Forks: 1

ChristophReich1996/Cell-DETR

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

Language: Python - Size: 32.9 MB - Last synced: 4 days ago - Pushed: about 2 years ago - Stars: 97 - Forks: 23

stardist/stardist-napari

StarDist plugin for napari

Language: Python - Size: 1.67 MB - Last synced: about 1 month ago - Pushed: about 1 month ago - Stars: 32 - Forks: 10

BartvanderWoude/Complexity-pretext-task-on-organoid-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.

Language: Python - Size: 3.89 MB - Last synced: about 1 month ago - Pushed: about 1 month ago - Stars: 1 - Forks: 0

mberkay0/segmentation_models.pytorch Fork of qubvel/segmentation_models.pytorch

Segmentation models with pretrained backbones. PyTorch. for Google Colab cell motility segmentation example.

Language: Python - Size: 5.6 MB - Last synced: about 1 month ago - Pushed: over 1 year ago - Stars: 0 - Forks: 0

TechAvi-eng/cell-image-analysis

Cell image analysis pipeline for RPE cell identification, counting and maturity classification

Language: Python - Size: 890 MB - Last synced: about 1 month ago - Pushed: about 1 month ago - Stars: 1 - Forks: 0

nadeemlab/DeepLIIF

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

Language: Python - Size: 91.2 MB - Last synced: about 1 month ago - Pushed: about 2 months ago - Stars: 132 - Forks: 52

oist/Usiigaci

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

Language: Jupyter Notebook - Size: 459 MB - Last synced: 19 days ago - Pushed: over 3 years ago - Stars: 188 - Forks: 70

qupath/qupath

QuPath - Bioimage analysis & digital pathology

Language: Java - Size: 93.5 MB - Last synced: about 1 month ago - Pushed: about 2 months ago - Stars: 962 - Forks: 267

mberkay0/ConvNeXt-MaskRCNN

Train torchvision's MaskRCNN model using the ConvNeXt architecture as the backbone network.

Language: Python - Size: 224 KB - Last synced: about 1 month ago - Pushed: over 1 year ago - Stars: 8 - Forks: 0

ChristophReich1996/Yeast-in-Microstructures-Dataset

Official and maintained implementation of the dataset paper "An Instance Segmentation Dataset of Yeast Cells in Microstructures" [EMBC 2023].

Language: Python - Size: 14.5 MB - Last synced: 14 days ago - Pushed: 3 months ago - Stars: 12 - Forks: 1

Lee-Gihun/MEDIAR

(NeurIPS 2022 CellSeg Challenge - 1st Winner) Open source code for "MEDIAR: Harmony of Data-Centric and Model-Centric for Multi-Modality Microscopy"

Language: Python - Size: 15 MB - Last synced: about 2 months ago - Pushed: about 2 months ago - Stars: 112 - Forks: 21

Omid-Nejati/BEFUnet

A Hybrid CNN-Transformer Architecture for Precise Medical Image Segmentation

Language: Python - Size: 1.03 MB - Last synced: about 2 months ago - Pushed: about 2 months ago - Stars: 9 - Forks: 1

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.

Language: Python - Size: 60 MB - Last synced: about 2 months ago - Pushed: about 2 months ago - Stars: 0 - Forks: 0

amirhossein-kz/HiFormer

HiFormer: Hierarchical Multi-scale Representations Using Transformers for Medical Image Segmentation (WACV 2023)

Language: Jupyter Notebook - Size: 6.18 MB - Last synced: 2 months ago - Pushed: 2 months ago - Stars: 106 - Forks: 19

wanglab-broad/ClusterMap

ClusterMap for multi-scale clustering analysis of spatial gene expression

Language: Jupyter Notebook - Size: 170 MB - Last synced: 2 months ago - Pushed: 2 months ago - Stars: 37 - Forks: 11

Mmasoud1/HistoJS

HistoJS: Web-Based Analytical Tool for Multiplexed Images. Limited Github Online Demo 👇

Language: JavaScript - Size: 290 MB - Last synced: 3 months ago - Pushed: 3 months ago - Stars: 10 - Forks: 0

BMCV/SuperDSM

SuperDSM is a globally optimal segmentation method based on superadditivity and deformable shape models for cell nuclei in fluorescence microscopy images and beyond.

Language: Python - Size: 41.7 MB - Last synced: 2 months ago - Pushed: 2 months ago - Stars: 2 - Forks: 0

SPerrott22/Deepcell-to-QuPath

pipeline that converts Deepcell generated instance segmentation masks of nuclei from an ome-tiff to Cell Objects with auto-generated cytoplasms in QuPath

Language: Jupyter Notebook - Size: 37 MB - Last synced: 3 months ago - Pushed: 3 months ago - Stars: 0 - Forks: 0

WenChentao/Seg2Link

Napari-based 3D cell segmentation software using machine learning predictions as inputs, especially for EM image stacks of brains

Language: Python - Size: 103 MB - Last synced: 21 days ago - Pushed: 9 months ago - Stars: 5 - Forks: 1

LiuLab-Bioelectronics-Harvard/ClusterMap

ClusterMap for multi-scale clustering analysis of spatial gene expression

Language: Jupyter Notebook - Size: 300 MB - Last synced: 6 months ago - Pushed: over 2 years ago - Stars: 6 - Forks: 2

kostrykin/rfove

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

Language: MATLAB - Size: 377 KB - Last synced: 3 months ago - Pushed: 3 months ago - Stars: 1 - Forks: 0

amatov/SegmentionCellEdge

Language: MATLAB - Size: 636 KB - Last synced: 6 months ago - Pushed: 6 months ago - Stars: 0 - Forks: 0

clintyr/bio-image-analysis

Example workflows for image processing, segmentation and analysis. Stitching and alignment functions also implemented.

Language: Jupyter Notebook - Size: 47.2 MB - Last synced: 4 months ago - Pushed: 6 months ago - Stars: 1 - Forks: 0

hip-satomi/SegServe

Language: Python - Size: 42 KB - Last synced: 6 months ago - Pushed: 6 months ago - Stars: 0 - Forks: 0

simonguld/CellSegmentationTracker

A Python module intended to make cell segmentation, tracking and subsequent (mostly biophysical) statisticial analysis easy

Language: Jupyter Notebook - Size: 1.8 GB - Last synced: 5 months ago - Pushed: 5 months ago - Stars: 5 - Forks: 1

RaiBP/cell-estimator

Project for the Applied Machine Learning (EI70360) class at TUM Summer Semester 2023.

Language: Python - Size: 79.6 MB - Last synced: 7 months ago - Pushed: 7 months ago - Stars: 0 - Forks: 0

UmutSahinSE/CellRecognition

A python script which is used for segmenting cells from provided phase contrast images. This is a university project.

Language: Python - Size: 87.3 MB - Last synced: 7 months ago - Pushed: almost 5 years ago - Stars: 4 - Forks: 0

christianrickert/CU-CellSeg

Cell segmentation of multi-channel images

Language: ImageJ Macro - Size: 201 MB - Last synced: 7 months ago - Pushed: about 1 year ago - Stars: 3 - Forks: 0

atakehiro/GUI_ROI_tool

the GUI tool for taking a region of interest (ROI) from a fluorescence image

Language: MATLAB - Size: 14.6 MB - Last synced: 7 months ago - Pushed: almost 4 years ago - Stars: 1 - Forks: 0

alexiaales/SpotitPy

An automated tool for Object-based colocalization in fluorescence microscopy images.

Language: Python - Size: 25.7 MB - Last synced: 7 months ago - Pushed: 8 months ago - Stars: 3 - Forks: 1

SaadUllahAkram/cpn

(Biological) Cell Proposal Network for Microscopy Image Analysis

Language: Matlab - Size: 85 KB - Last synced: 7 months ago - Pushed: about 7 years ago - Stars: 8 - Forks: 0

poloarol/snakemake-vizgen-cell-segmentation

A snakemake pipeline to perform cell segmentation on MERFISH spatial transcriptomics data.

Language: Python - Size: 13.7 KB - Last synced: 6 months ago - Pushed: 6 months ago - Stars: 0 - Forks: 0

allchanzi/CellAnalyzer

Application for cell segmentation and analysis

Language: Python - Size: 211 MB - Last synced: 7 months ago - Pushed: almost 6 years ago - Stars: 0 - Forks: 0

NormanTrinh/cell-segmentation

Cell segmentation using Mask R-CNN Pytorch

Language: Jupyter Notebook - Size: 4.41 MB - Last synced: 7 months ago - Pushed: 7 months ago - Stars: 0 - Forks: 0

epitools/epitools

Quantifying 2D cell shape and epithelial tissue dynamics

Language: Python - Size: 115 MB - Last synced: 28 days ago - Pushed: 8 months ago - Stars: 6 - Forks: 0

orukundo/Tool-for-Evaluating-Deep-Learning-Models-in-Histopathological-Image-Analysis

Tool for Evaluating Deep Learning Models in Histopathological Image Analysis - A MATLAB-based User Interface [Preliminary/Tentative Version]

Language: MATLAB - Size: 76.2 KB - Last synced: 8 months ago - Pushed: 8 months ago - Stars: 0 - Forks: 0

yaoguangluo/ETL_Unicorn

数据可视化, 数据挖掘, 数据处理 ETL分析

Language: Java - Size: 1.52 MB - Last synced: 7 months ago - Pushed: over 2 years ago - Stars: 167 - Forks: 78

ChristophReich1996/TYC-Dataset

Official and maintained implementation of the dataset paper "The TYC Dataset for Understanding Instance-Level Semantics and Motions of Cells in Microstructures" [ICCVW 2023].

Language: Python - Size: 1.44 MB - Last synced: 12 days ago - Pushed: 9 months ago - Stars: 2 - Forks: 2

ciccalab/SIMPLI

SIMPLI is a highly configurable pipeline for the analysis of multiplexed imaging data.

Language: R - Size: 45.2 MB - Last synced: 9 months ago - Pushed: 11 months ago - Stars: 26 - Forks: 4

jendelel/CellCounter

A small GUI application for counting cells in microscope images

Language: Python - Size: 3.91 KB - Last synced: 10 months ago - Pushed: over 5 years ago - Stars: 5 - Forks: 0

rickyota/CSML

Cell Segmenter using Machine Learning

Language: Python - Size: 21.9 MB - Last synced: 7 months ago - Pushed: 10 months ago - Stars: 9 - Forks: 1

RaiBP/cellestimator

Segment, classify and label blood cell images. Project for the Applied Machine Intelligence course at the Technical University of Munich (TUM), Summer Semester 2023.

Language: Python - Size: 78.4 MB - Last synced: 10 months ago - Pushed: 10 months ago - Stars: 0 - Forks: 1

aws-samples/amazon-sagemaker-cell-segmentation-workshop

This workshop outlines a machine-learning cell segmentation architecture from scratch for the life-sciences vertical, using Amazon SageMaker, S3, Lambda and SageMaker Inference endpoints

Language: Jupyter Notebook - Size: 528 KB - Last synced: 10 months ago - Pushed: 10 months ago - Stars: 4 - Forks: 0

pywood21/po_mfa_2023

Application of polarized optical microscopy-based MFA imaging and semantic segmentation-based cell-by-cell anatomy measurement to hardwoods having various anatomical characteristics

Language: Jupyter Notebook - Size: 19 MB - Last synced: 11 months ago - Pushed: 11 months ago - Stars: 1 - Forks: 0

Rajaguhan437/Cell_Detect-Quantitative-Representation

Cell Detection and Cell Segmentation

Language: Jupyter Notebook - Size: 81.8 MB - Last synced: 11 months ago - Pushed: 11 months ago - Stars: 0 - Forks: 0

nthndy/cell-comp-analysis

Analysis for cell competition phd project

Language: Jupyter Notebook - Size: 134 MB - Last synced: 12 months ago - Pushed: 12 months ago - Stars: 0 - Forks: 0

ariel-waisman/LabelsToROIs

A Fiji/ImageJ plugin to generate ROIs from label images, allowing ROI erosion and quantification

Language: Python - Size: 2.02 MB - Last synced: 7 months ago - Pushed: over 2 years ago - Stars: 17 - Forks: 8

Lewislou/cellseg-sribd

The code implementation for cell segmentation

Language: Python - Size: 256 KB - Last synced: 8 months ago - Pushed: 10 months ago - Stars: 4 - Forks: 0

farkoo/Cells-Segmentation-and-Count

This program is implemented to count the number of cells in the image. The cells are also labeled and the perimeter and area are calculated for each cell.

Language: MATLAB - Size: 348 KB - Last synced: 11 months ago - Pushed: almost 3 years ago - Stars: 5 - Forks: 2

NiharJani2002/CSE-523-Machine-Learning

I am pursuing Machine Learning Course at Ahmedabad University. This Repository contains the Code and Dataset, of the paper to be Reproduced during this course.

Language: Jupyter Notebook - Size: 36.9 MB - Last synced: about 1 year ago - Pushed: about 1 year ago - Stars: 1 - Forks: 0

mberkay0/cell-segmentation-with-machine-learning

It is a study that compares machine learning and deep learning methods in shallow data for the cell segmentation problem.

Language: Jupyter Notebook - Size: 4.96 MB - Last synced: about 1 month ago - Pushed: over 1 year ago - Stars: 1 - Forks: 1

YAI-Medical/cancer-instance-segmentation-from-tissue 📦

Tissue Segmentation of Cancer using DeepLabV3 + Resnet101, U-Net, Inception U-Net, RefineNet

Language: Python - Size: 2.66 MB - Last synced: about 1 year ago - Pushed: almost 2 years ago - Stars: 16 - Forks: 6

AntonotnaWang/3DCellSeg

Official implementation of "A novel deep learning-based 3D cell segmentation framework for future image-based disease detection". (However, I think the title should be "3DCellSeg - a robust deep learning-based 3D cell instance segmentation pipeline".)

Language: Jupyter Notebook - Size: 21.4 MB - Last synced: about 1 year ago - Pushed: about 2 years ago - Stars: 9 - Forks: 3

canfkoyuncu/IterativeHMinima

Iterative H-minima Based Marker-Controlled Watershed for Cell Nucleus Segmentation

Language: Matlab - Size: 420 KB - Last synced: about 1 year ago - Pushed: about 7 years ago - Stars: 11 - Forks: 1

hip-satomi/ObiWan-Microbi

Omero based integrated Workflow for annotating Microbes in the Cloud

Language: Dockerfile - Size: 12.4 MB - Last synced: 6 months ago - Pushed: 6 months ago - Stars: 4 - Forks: 1

g0thic/Rep1

Size: 3.31 MB - Last synced: about 1 year ago - Pushed: over 1 year ago - Stars: 0 - Forks: 0

marshuang80/cell-segmentation

PyTorch implementation of several neural network models for cellular image segmentation

Language: Jupyter Notebook - Size: 40.3 MB - Last synced: about 1 year ago - Pushed: over 4 years ago - Stars: 43 - Forks: 7

mr-ravin/unet-image-segmentation 📦

This repository contains the Unet architecture built with Pytorch library. Here, the Unet architecture is used to perform the image segmentation.

Language: Python - Size: 351 KB - Last synced: about 1 year ago - Pushed: over 2 years ago - Stars: 0 - Forks: 0

hip-satomi/microbeSEG

Deep learning-based instance segmentation tool for roundish objects in 2D and 2D+t data

Language: Python - Size: 8.44 MB - Last synced: about 1 year ago - Pushed: over 1 year ago - Stars: 4 - Forks: 1

SAIL-GuoLab/Cell_Segmentation_and_Tracking

For cell segmentation and tracking.

Language: Jupyter Notebook - Size: 214 MB - Last synced: about 1 year ago - Pushed: about 4 years ago - Stars: 31 - Forks: 5

pywood21/po_mfa_2022

A new CV technique combining polarization optical microscopy, fluorescence microscopy, and image segmentation

Language: Jupyter Notebook - Size: 5.72 MB - Last synced: 12 months ago - Pushed: over 1 year ago - Stars: 1 - Forks: 0

RnR-2018/BMEN4460-NB1-simple_cell_segmentation_with_a_single_layered_perceptron

Child repository of Deep-learning-with-PyTorch-and-GCP

Language: Jupyter Notebook - Size: 11 MB - Last synced: about 1 year ago - Pushed: over 4 years ago - Stars: 7 - Forks: 0

TimScherr/KIT-GE-3-Cell-Segmentation-for-CTC

Distance-transform-prediction-based segmentation method used for our submission to the 6th edition of the ISBI Cell Tracking Challenge 2021 as team KIT-Sch-GE (2) (now KIT-GE (3)).

Language: Jupyter Notebook - Size: 735 KB - Last synced: about 1 year ago - Pushed: over 1 year ago - Stars: 0 - Forks: 2

iitmcvg/Cell-Segmentation

Automated identification of cell boundaries from the pathological video data

Language: Python - Size: 24.9 MB - Last synced: about 1 year ago - Pushed: almost 6 years ago - Stars: 22 - Forks: 9

alzbeta-hrdlickova/cell-segmentation

Cell segmentation using convolutional natural networks

Language: Python - Size: 747 KB - Last synced: about 1 year ago - Pushed: almost 2 years ago - Stars: 0 - Forks: 0

jlifferth/HCC_analysis

Research project to track movement of Hepatoceullar Carcinoma cells.

Language: Jupyter Notebook - Size: 116 MB - Last synced: about 1 year ago - Pushed: about 2 years ago - Stars: 0 - Forks: 0

KeesStraatman/WGA-analysis

ImageJ macros to identify cell area in WGA stained and other cell membrane stained cells

Size: 337 KB - Last synced: 11 months ago - Pushed: over 2 years ago - Stars: 0 - Forks: 0

Jesse-McDonald/CASTER

Computer Assisted Segmentation Tool Environment Revisit

Language: Processing - Size: 110 MB - Last synced: about 1 year ago - Pushed: over 3 years ago - Stars: 1 - Forks: 1

anmartinezs/polyqIB

Software developed to analyze how polyQ inclusion bodies interact with ER membranes in situ

Language: Python - Size: 189 KB - Last synced: about 1 year ago - Pushed: over 4 years ago - Stars: 3 - Forks: 3

wufeim/breast-cancer

Breast Cancer Analysis

Language: Python - Size: 37.1 KB - Last synced: about 1 year ago - Pushed: almost 5 years ago - Stars: 1 - Forks: 0

haelbouhad/imagej-plugin-uv-characterization

Language: Java - Size: 88.9 KB - Last synced: about 1 year ago - Pushed: about 7 years ago - Stars: 1 - Forks: 0

pedrodiamel/sicklemia-cell-segmentation

sicklemia-cell segmentation

Language: Matlab - Size: 12.7 MB - Last synced: about 1 year ago - Pushed: about 7 years ago - Stars: 1 - Forks: 0

adamjstewart/cell_segmentation

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

Language: Python - Size: 80.1 KB - Last synced: about 1 year ago - Pushed: about 5 years ago - Stars: 1 - Forks: 0

vrrenske/spotprocessR

code used in van Raaphorst, Kjos & Veening (2017), Chromosome segregation drives division site selection in Streptococcus pneumoniae, PNAS

Language: R - Size: 32.2 KB - Last synced: about 1 year ago - Pushed: about 6 years ago - Stars: 2 - Forks: 1