qupath/qupath

QuPath - Open-source bioimage analysis for research

Language: Java - Size: 97.4 MB - Last synced at: about 12 hours ago - Pushed at: about 12 hours ago - Stars: 1,149 - Forks: 298

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)

Language: HTML - Size: 36.2 MB - Last synced at: 2 days ago - Pushed at: 2 days ago - Stars: 4 - Forks: 0

royerlab/ultrack

Cell tracking and segmentation software

Language: Python - Size: 93.9 MB - Last synced at: 2 days ago - Pushed at: 2 days ago - Stars: 113 - Forks: 16

TissueImageAnalytics/tiatoolbox

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

Language: Python - Size: 505 MB - Last synced at: 1 day ago - Pushed at: 1 day ago - Stars: 425 - Forks: 89

KevinCortacero/Kartezio

Evolve your OpenCV Image Processing filters using Cartesian Genetic Programming

Language: Python - Size: 518 KB - Last synced at: 3 days ago - Pushed at: 3 days ago - Stars: 33 - Forks: 6

okunator/cellseg_models.pytorch

Encoder-Decoder Cell and Nuclei segmentation models

Language: Python - Size: 101 MB - Last synced at: 3 days ago - Pushed at: 3 days ago - Stars: 91 - Forks: 4

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]

Language: Python - Size: 94.3 MB - Last synced at: 3 days ago - Pushed at: 11 days ago - Stars: 193 - Forks: 76

EliHei2/segger_dev

a cutting-edge cell segmentation model specifically designed for single-molecule resolved spatial omics datasets. It addresses the challenge of accurately segmenting individual cells in complex imaging datasets, leveraging a unique approach based on graph neural networks (GNNs).

Language: Python - Size: 5.41 MB - Last synced at: 5 days ago - Pushed at: 5 days ago - Stars: 61 - Forks: 6

Jesse-McDonald/CASTER

Computer Assisted Segmentation Tool Environment Revisit

Language: Processing - Size: 110 MB - Last synced at: 5 days ago - Pushed at: 5 days ago - Stars: 1 - Forks: 1

computational-cell-analytics/micro-sam

Segment Anything for Microscopy

Language: Jupyter Notebook - Size: 51.7 MB - Last synced at: 5 days ago - Pushed at: 5 days ago - Stars: 534 - Forks: 67

MouseLand/cellpose

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

Language: Jupyter Notebook - Size: 117 MB - Last synced at: 6 days ago - Pushed at: 6 days ago - Stars: 1,591 - Forks: 449

joda01/imagec

imageC / EVAnalyzer2 - High throughput biological image processor

Language: C++ - Size: 705 MB - Last synced at: 6 days ago - Pushed at: 6 days ago - Stars: 4 - Forks: 1

stardist/stardist

StarDist - Object Detection with Star-convex Shapes

Language: Python - Size: 114 MB - Last synced at: 5 days ago - Pushed at: 7 months ago - Stars: 1,026 - Forks: 240

royerlab/ultrack-atini-2025

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

Size: 27.1 MB - Last synced at: 8 days ago - Pushed at: 8 days ago - Stars: 0 - Forks: 0

unikill066/spinal_cord_cell_segmentation

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

Language: Python - Size: 15.6 KB - Last synced at: 11 days ago - Pushed at: 11 days ago - Stars: 0 - 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 at: 14 days ago - Pushed at: 14 days ago - Stars: 3 - 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 at: 16 days ago - Pushed at: 16 days ago - Stars: 13 - Forks: 2

FZJ-INM1-BDA/celldetection

Scalable Instance Segmentation using PyTorch & PyTorch Lightning.

Language: Python - Size: 15.4 MB - Last synced at: 17 days ago - Pushed at: 17 days ago - Stars: 133 - Forks: 21

ChenLiu-1996/DiffKillR

[ICASSP 2025 Oral] DiffKillR: Killing and Recreating Diffeomorphisms for Cell Annotation in Dense Microscopy Images

Language: Python - Size: 5.33 MB - Last synced at: 4 days ago - Pushed at: 18 days ago - Stars: 2 - Forks: 0

aristoteleo/spateo-release

Spatiotemporal modeling of spatial transcriptomics

Language: Python - Size: 33.9 MB - Last synced at: 14 days ago - Pushed at: about 2 months ago - Stars: 281 - Forks: 36

epitools/epitools

Quantifying 2D cell shape and epithelial tissue dynamics

Language: Python - Size: 115 MB - Last synced at: 7 days ago - Pushed at: 3 months ago - Stars: 7 - Forks: 0

nadeemlab/ImPartial

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

Language: Python - Size: 174 MB - Last synced at: about 1 month ago - Pushed at: about 1 month ago - Stars: 39 - Forks: 3

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 at: 3 days ago - Pushed at: about 3 years ago - Stars: 101 - Forks: 23

KrishnaswamyLab/DiffKillR

[ICASSP 2025 Oral] DiffKillR: Killing and Recreating Diffeomorphisms for Cell Annotation in Dense Microscopy Images

Language: Python - Size: 5.28 MB - Last synced at: 4 days ago - Pushed at: about 1 month ago - Stars: 5 - Forks: 0

PraiseTheDarkFlo/CellSePi

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

Language: Python - Size: 46.5 MB - Last synced at: 19 days ago - Pushed at: about 2 months ago - Stars: 1 - Forks: 0

stardist/stardist-napari

StarDist plugin for napari

Language: Python - Size: 1.69 MB - Last synced at: 29 days ago - Pushed at: 9 months ago - Stars: 38 - Forks: 11

berkyalcinkaya/yeastvision

Deep-learning enabled quantitative image analysis of cell full lifecycles

Language: Python - Size: 367 MB - Last synced at: 13 days ago - Pushed at: about 2 months ago - Stars: 4 - Forks: 2

cjrobinson8/Complex-Wound-Analysis-using-AI

Repository for publication outlining a number of computational models for complex wound analysis in both mice and humans.

Size: 8.79 KB - Last synced at: about 2 months ago - Pushed at: about 2 months ago - Stars: 0 - Forks: 0

DanuserLab/u-segment3D

Generate consensus 3D cells segmentations by combining 2D cell segmentations from any combination of xy, xz, yz views, compatible with outputs of any 2D segmentation method.

Language: MATLAB - Size: 77.8 MB - Last synced at: 26 days ago - Pushed at: 2 months ago - Stars: 16 - Forks: 4

kdha0727/cancer-instance-segmentation-from-tissue

Tissue Cancer Segmentation project using multiple segmentation networks

Language: Python - Size: 2.66 MB - Last synced at: 5 days ago - Pushed at: almost 3 years ago - Stars: 23 - Forks: 2

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: 12.7 MB - Last synced at: about 2 months ago - Pushed at: about 2 months ago - Stars: 1 - Forks: 0

amatov/SegmentionCellEdge

Language: MATLAB - Size: 642 KB - Last synced at: 2 months ago - Pushed at: 2 months ago - Stars: 0 - Forks: 0

tuguiMAtei/Complex-Wound-Analysis-using-AI

Repository for publication outlining a number of computational models for complex wound analysis in both mice and humans.

Size: 1.95 KB - Last synced at: 2 months ago - Pushed at: 2 months ago - Stars: 0 - Forks: 0

yash-gajjjar/post-HCT-Survival-Predictions

Improve prediction of transplant survival rates equitably for allogeneic HCT patients

Language: Jupyter Notebook - Size: 2.05 MB - Last synced at: 2 months ago - Pushed at: 2 months ago - Stars: 1 - Forks: 0

baltuni/Calcium-Correlation-Tool Fork of Angsas/Calcium-Correlation-Tool

Cell segmentation and tracking pipeline for time-lapse microscopy data using Cellpose. Includes segmentation, tracking, and correlation analysis of cell properties over time.

Language: Jupyter Notebook - Size: 1.41 MB - Last synced at: 2 months ago - Pushed at: 2 months ago - Stars: 3 - Forks: 0

WEHI-SODA-Hub/spatialvpt

Segmentation and QC workflow for MERSCOPE using vizgen-postprocessing tool

Language: Nextflow - Size: 418 KB - Last synced at: 3 days ago - Pushed at: 3 days ago - Stars: 0 - Forks: 0

oist/Usiigaci

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

Language: Jupyter Notebook - Size: 459 MB - Last synced at: 3 days ago - Pushed at: over 4 years ago - Stars: 195 - Forks: 68

SAIL-GuoLab/Cell_Segmentation_and_Tracking

For cell segmentation and tracking.

Language: Jupyter Notebook - Size: 214 MB - Last synced at: 4 days ago - Pushed at: about 5 years ago - Stars: 36 - Forks: 5

Mmasoud1/HistoJS

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

Language: JavaScript - Size: 290 MB - Last synced at: 7 days ago - Pushed at: about 1 year ago - Stars: 19 - Forks: 0

tlo-bot/omnisegger

OmniSegger - from the Wiggins Lab at UW

Language: MATLAB - Size: 74.3 MB - Last synced at: 4 months ago - Pushed at: 4 months ago - Stars: 9 - Forks: 4

hip-satomi/SegServe

Language: Python - Size: 42 KB - Last synced at: 4 months ago - Pushed at: 4 months ago - Stars: 0 - 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 at: 28 days ago - Pushed at: about 1 year ago - Stars: 14 - Forks: 0

Potescito/Self-Supervised-Learning-for-Cell-Segmentation

A simple, step-by-step guide to applying self-supervised learning techniques to a mitochondria segmentation task using PyTorch.

Language: Jupyter Notebook - Size: 2.94 MB - Last synced at: 4 months ago - Pushed at: 4 months ago - Stars: 0 - Forks: 0

sejal-prog/Cell-Tracking

Proposal - Leverage the Segment Anything Model (SAM) to enable promptable image segmentation, facilitating a highly adaptable and precise approach for identifying diverse cellular structures.

Size: 6.55 MB - Last synced at: 4 months ago - Pushed at: 4 months ago - Stars: 0 - Forks: 0

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: 60.1 MB - Last synced at: 2 months ago - Pushed at: 5 months ago - Stars: 0 - Forks: 0

NIGMS/Biomedical-Imaging-Analysis-using-AI-ML-Approaches

Machine Learning module for cloud-based analyses developed as part of the NIGMS Sandbox Project

Language: Jupyter Notebook - Size: 24.4 MB - Last synced at: 2 months ago - Pushed at: 2 months ago - Stars: 4 - Forks: 4

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 at: 28 days ago - Pushed at: over 1 year ago - Stars: 5 - Forks: 2

marshuang80/cell-segmentation

PyTorch implementation of several neural network models for cellular image segmentation

Language: Jupyter Notebook - Size: 40.3 MB - Last synced at: 27 days ago - Pushed at: over 5 years ago - Stars: 47 - Forks: 7

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: 42.2 MB - Last synced at: 4 months ago - Pushed at: 4 months ago - Stars: 3 - Forks: 0

arnaublanco/Fluospotter

Fluospotter is an end-to-end pipeline designed for nuclei segmentation and puncta detection in fluorescence microscopy images.

Language: Python - Size: 56.3 MB - Last synced at: about 1 month ago - Pushed at: 7 months ago - Stars: 2 - Forks: 0

himsr-lab/CU-CellSeg

Cell segmentation of multi-channel images

Language: ImageJ Macro - Size: 201 MB - Last synced at: about 2 months ago - Pushed at: about 2 years ago - Stars: 4 - Forks: 0

wanglab-broad/ClusterMap

ClusterMap for multi-scale clustering analysis of spatial gene expression

Language: Jupyter Notebook - Size: 171 MB - Last synced at: 5 months ago - Pushed at: 10 months ago - Stars: 41 - Forks: 11

LSeu-Open/Cellpose_Gradio

A Gradio based user-friendly interface for cell segmentation using Cellpose

Language: Python - Size: 2.24 MB - Last synced at: 8 months ago - Pushed at: 8 months ago - Stars: 1 - Forks: 0

AllenNeuralDynamics/aind-large-scale-cellpose

Large-scale cell segmentation with cellpose.

Language: Python - Size: 120 KB - Last synced at: 7 months ago - Pushed at: 7 months ago - Stars: 4 - Forks: 0

canfkoyuncu/IterativeHMinima

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

Language: Matlab - Size: 420 KB - Last synced at: about 2 months ago - Pushed at: about 8 years ago - Stars: 12 - Forks: 1

joanabaiao/cell-segmentation

This project implements cell segmentation and classification of red and white blood cells using the YOLOv8 model.

Language: Jupyter Notebook - Size: 63.1 MB - Last synced at: 9 months ago - Pushed at: 9 months ago - Stars: 0 - Forks: 0

JostTim/CellReg Fork of zivlab/CellReg

Registration of cells across sessions.

Language: MATLAB - Size: 17.3 MB - Last synced at: 10 months ago - Pushed at: 10 months ago - Stars: 0 - Forks: 0

JostTim/suite2p Fork of MouseLand/suite2p

cell detection in calcium imaging recordings

Language: Jupyter Notebook - Size: 90.6 MB - Last synced at: 18 days ago - Pushed at: about 1 year 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 at: 10 months ago - Pushed at: over 1 year ago - Stars: 5 - Forks: 1

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 at: 11 months ago - Pushed at: over 2 years ago - Stars: 7 - Forks: 1

Omid-Nejati/BEFUnet

A Hybrid CNN-Transformer Architecture for Precise Medical Image Segmentation

Language: Python - Size: 1.03 MB - Last synced at: 11 months ago - Pushed at: 11 months ago - Stars: 20 - Forks: 4

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 at: 12 months ago - Pushed at: 12 months ago - Stars: 46 - Forks: 2

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 at: about 1 year ago - Pushed at: about 1 year ago - Stars: 1 - Forks: 0

lstrgar/SEG

Evaluation of label free cell and nuclei segmentation

Language: Jupyter Notebook - Size: 19.1 MB - Last synced at: 12 months ago - Pushed at: 12 months ago - Stars: 6 - Forks: 3

Curovearth/Cell-Segmentation

Cell segmentation performed as part of Digital Image Processing course.

Language: Jupyter Notebook - Size: 64.6 MB - Last synced at: about 1 year ago - Pushed at: over 2 years ago - Stars: 0 - Forks: 1

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 at: about 1 year ago - Pushed at: over 2 years 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 at: about 1 year ago - Pushed at: about 1 year ago - Stars: 1 - Forks: 0

mberkay0/ConvNeXt-MaskRCNN

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

Language: Python - Size: 224 KB - Last synced at: about 1 year ago - Pushed at: over 2 years ago - Stars: 8 - Forks: 0

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 at: about 1 year ago - Pushed at: about 1 year ago - Stars: 112 - Forks: 21

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 at: about 1 year ago - Pushed at: about 1 year ago - Stars: 106 - Forks: 19

LiuLab-Bioelectronics-Harvard/ClusterMap

ClusterMap for multi-scale clustering analysis of spatial gene expression

Language: Jupyter Notebook - Size: 300 MB - Last synced at: 5 months ago - Pushed at: about 3 years ago - Stars: 7 - Forks: 2

adamjstewart/cell_segmentation

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

Language: Python - Size: 80.1 KB - Last synced at: about 1 month ago - Pushed at: about 6 years ago - Stars: 2 - Forks: 0

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 at: 27 days ago - Pushed at: about 1 year ago - Stars: 10 - Forks: 2

Rajaguhan437/Cell_Detect-Quantitative-Representation

Cell Detection and Cell Segmentation

Language: Jupyter Notebook - Size: 81.8 MB - Last synced at: 2 months ago - Pushed at: almost 2 years ago - Stars: 2 - Forks: 0

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 at: 3 months ago - Pushed at: about 1 year ago - Stars: 1 - 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 at: over 1 year ago - Pushed at: over 1 year ago - Stars: 1 - Forks: 0

RaiBP/cell-estimator

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

Language: Python - Size: 79.6 MB - Last synced at: over 1 year ago - Pushed at: over 1 year 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 at: over 1 year ago - Pushed at: almost 6 years ago - Stars: 4 - 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 at: over 1 year ago - Pushed at: almost 5 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 at: over 1 year ago - Pushed at: over 1 year ago - Stars: 3 - Forks: 1

SaadUllahAkram/cpn

(Biological) Cell Proposal Network for Microscopy Image Analysis

Language: Matlab - Size: 85 KB - Last synced at: over 1 year ago - Pushed at: almost 8 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 at: over 1 year ago - Pushed at: over 1 year ago - Stars: 0 - Forks: 0

allchanzi/CellAnalyzer

Application for cell segmentation and analysis

Language: Python - Size: 211 MB - Last synced at: over 1 year ago - Pushed at: almost 7 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 at: over 1 year ago - Pushed at: over 1 year ago - Stars: 0 - 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 at: over 1 year ago - Pushed at: over 1 year 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 at: over 1 year ago - Pushed at: about 3 years ago - Stars: 167 - Forks: 78

ciccalab/SIMPLI

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

Language: R - Size: 45.2 MB - Last synced at: over 1 year ago - Pushed at: almost 2 years 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 at: almost 2 years ago - Pushed at: about 6 years ago - Stars: 5 - Forks: 0

rickyota/CSML

Cell Segmenter using Machine Learning

Language: Python - Size: 21.9 MB - Last synced at: over 1 year ago - Pushed at: almost 2 years 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 at: almost 2 years ago - Pushed at: almost 2 years 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 at: almost 2 years ago - Pushed at: almost 2 years 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 at: almost 2 years ago - Pushed at: almost 2 years ago - Stars: 1 - Forks: 0

nthndy/cell-comp-analysis

Analysis for cell competition phd project

Language: Jupyter Notebook - Size: 134 MB - Last synced at: almost 2 years ago - Pushed at: almost 2 years 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 at: over 1 year ago - Pushed at: over 3 years ago - Stars: 17 - Forks: 8

Lewislou/cellseg-sribd

The code implementation for cell segmentation

Language: Python - Size: 256 KB - Last synced at: over 1 year ago - Pushed at: almost 2 years 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 at: almost 2 years ago - Pushed at: almost 4 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 at: about 2 years ago - Pushed at: about 2 years 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 at: about 1 year ago - Pushed at: over 2 years ago - Stars: 1 - Forks: 1

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 at: about 2 years ago - Pushed at: about 3 years ago - Stars: 9 - Forks: 3

jpviguerasguillen/corneal_endothelium_TVST

Deep learning method presented in the Translational Vision Science & Technology (TVST) journal to segment cells from corneal endothelium images obtained with specular microscopy and subsequently infer the corneal parameters.

Language: Jupyter Notebook - Size: 489 KB - Last synced at: 6 days ago - Pushed at: about 3 years ago - Stars: 2 - Forks: 1