sanderslab/magellanmapper

MagellanMapper is a graphical interface for 3D bioimage annotation, atlas registration, and regional quantification

Language: Python - Size: 8.13 MB - Last synced: 3 days ago - Pushed: 3 days ago - Stars: 20 - Forks: 3

mahmoodlab/CONCH

A vision-language foundation model for computational pathology - Nature Medicine

Language: Python - Size: 1.2 MB - Last synced: 2 days ago - Pushed: about 2 months ago - Stars: 152 - Forks: 10

kreshuklab/plant-seg

A tool for cell instance aware segmentation in densely packed 3D volumetric images

Language: Python - Size: 172 MB - Last synced: 3 days ago - Pushed: 3 days ago - Stars: 86 - Forks: 30

ScalableCytometryImageProcessing/SCIP

Scalable Cytometry Image Processing (SCIP) is an open-source tool that implements an image processing pipeline on top of Dask, a distributed computing framework written in Python. SCIP performs projection, illumination correction, image segmentation and masking, and feature extraction.

Language: Python - Size: 20.5 MB - Last synced: 3 days ago - Pushed: 3 days ago - Stars: 7 - Forks: 0

stardist/stardist

StarDist - Object Detection with Star-convex Shapes

Language: Python - Size: 118 MB - Last synced: 2 days ago - Pushed: 28 days ago - Stars: 825 - Forks: 213

MontpellierRessourcesImagerie/imagej_macros_and_scripts

ImageJ macros and scripts written at the imaging facility MRI

Language: ImageJ Macro - Size: 7.02 MB - Last synced: 4 days ago - Pushed: 4 days ago - Stars: 27 - Forks: 14

hallvaaw/awesome-biological-image-analysis

A curated list of software, tools, pipelines, plugins etc. for image analysis related to biological questions.

Size: 401 KB - Last synced: 2 days ago - Pushed: 25 days ago - Stars: 96 - Forks: 19

mastodon-sc/mastodon

Mastodon – a large-scale tracking and track-editing framework for large, multi-view images.

Language: Java - Size: 16.6 MB - Last synced: 7 days ago - Pushed: 8 days ago - Stars: 64 - Forks: 20

bioimage-io/core-bioimage-io-python

Python libraries for loading, running and packaging bioimage.io models

Language: Jupyter Notebook - Size: 6.43 MB - Last synced: 9 days ago - Pushed: 9 days ago - Stars: 18 - Forks: 18

clEsperanto/pyclesperanto_prototype

GPU-accelerated bio-image analysis focusing on 3D+t microscopy image data

Language: Jupyter Notebook - Size: 221 MB - Last synced: 11 days ago - Pushed: 13 days ago - Stars: 197 - Forks: 45

lstrgar/SEG

Evaluation of label free cell and nuclei segmentation

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

danihae/bio-image-unet

U-Net implementation in PyTorch for segmentation of bio-images

Language: Python - Size: 218 KB - Last synced: 14 days ago - Pushed: 14 days ago - Stars: 2 - Forks: 0

dl4mia/DL4MIA_2024

Main repository gathering all content of the EMBO-DL4MIA 2024 course.

Language: Shell - Size: 32.2 KB - Last synced: 15 days ago - Pushed: 15 days ago - Stars: 1 - Forks: 1

4DNucleome/PartSeg

Tool for segmentation in bioimaging

Language: Python - Size: 32.5 MB - Last synced: 5 days ago - Pushed: 5 days ago - Stars: 27 - Forks: 7

VeraPancaldiLab/tysserand

Fast reconstruction of spatial networks from bioimages.

Language: Python - Size: 68.8 MB - Last synced: 9 days ago - Pushed: 19 days ago - Stars: 23 - Forks: 6

mahmoodlab/TOAD

AI-based pathology predicts origins for cancers of unknown primary - Nature

Language: Python - Size: 2.79 MB - Last synced: 17 days ago - Pushed: over 2 years ago - Stars: 167 - Forks: 44

haesleinhuepf/human-eval-bia

Benchmarking Large Language Models for Bio-Image Analysis Code Generation

Language: Jupyter Notebook - Size: 39.6 MB - Last synced: 10 days ago - Pushed: 12 days ago - Stars: 7 - Forks: 2

MercaderLabAnatomy/T-MIDAS

Automated batch processing for tissue microscopy image data

Language: Cool - Size: 302 KB - Last synced: about 1 month ago - Pushed: about 1 month ago - Stars: 3 - Forks: 1

matjesg/deepflash2

A deep-learning pipeline for segmentation of ambiguous microscopic images.

Language: Jupyter Notebook - Size: 207 MB - Last synced: 27 days ago - Pushed: 2 months ago - Stars: 57 - Forks: 9

qupath/qupath

QuPath - Bioimage analysis & digital pathology

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

arttumiettinen/pi2

C++ library and command-line software for processing and analysis of terabyte-scale volume images locally or on a computing cluster.

Language: C++ - Size: 4.03 MB - Last synced: 4 days ago - Pushed: 4 days ago - Stars: 48 - Forks: 12

mehta-lab/VisCy

computer vision models for single-cell phenotyping

Language: Python - Size: 3.87 MB - Last synced: 10 days ago - Pushed: 16 days ago - Stars: 16 - Forks: 2

ai4life-opencalls/oc_1_project_3

Ai4Life Open Call #1 - Project #3, semantic segmentation of kidney and heart tissue

Language: Jupyter Notebook - Size: 18.8 MB - Last synced: 2 months ago - Pushed: 2 months ago - Stars: 0 - Forks: 0

dmattek/ARCOS-tutorial

A Jupyter notebook to identify collective cell signalling in raw microscopy images

Language: Jupyter Notebook - Size: 2.93 MB - Last synced: 4 days ago - Pushed: 2 months ago - Stars: 1 - Forks: 0

ai4life-opencalls/oc-1-project-11

Open Call #1: Segmentation and Tracking of Epithelial Cells

Language: Jupyter Notebook - Size: 127 MB - Last synced: 2 months ago - Pushed: 2 months ago - Stars: 0 - Forks: 0

ai4life-opencalls/oc-1-project-6

Open Call #1: Murine Skeletal Muscle Analysis

Size: 37.4 MB - Last synced: 2 months ago - Pushed: 2 months ago - Stars: 0 - Forks: 0

romlambert/CytotoxPred

RF models for the prediction of cell viability in muscle cells from Cell Painting profiles.

Language: Jupyter Notebook - Size: 718 KB - Last synced: 4 months ago - Pushed: 4 months ago - Stars: 0 - Forks: 0

SOCR/3d-cell-morphometry

Source code and workflow protocols for SOCR 3D Cell Morphometry Project

Language: C - Size: 1.02 MB - Last synced: about 1 month ago - Pushed: almost 2 years ago - Stars: 2 - Forks: 0

Euro-BioImaging/OME_Zarr_Tools

Course materials for the practical on the Defragmentation Training School 2 - Porto, 8-12 May 2023

Language: Shell - Size: 7.46 MB - Last synced: 4 months ago - Pushed: 7 months ago - Stars: 2 - Forks: 0

tix209/TSOAX

Extraction and tracking of dynamic biopolymer networks.

Language: C++ - Size: 639 KB - Last synced: 7 months ago - Pushed: about 2 years ago - Stars: 2 - Forks: 1

RMS-DAIM/Python-for-Bioimage-Analysis

This is the repository for a Python bioimage analysis course which establishes the fundamentals of image analysis in the context of biological imaging.

Language: Jupyter Notebook - Size: 390 MB - Last synced: 7 months ago - Pushed: about 4 years ago - Stars: 121 - Forks: 39

leoguignard/Mouse-Atlas

Code for the article In toto imaging and reconstruction of post-implantation mouse development at the single-cell level

Language: Python - Size: 293 KB - Last synced: 7 months ago - Pushed: over 5 years ago - Stars: 0 - Forks: 0

multi-template-matching/MultiTemplateMatching-Fiji

Fiji plugin for object(s) detection using template(s) matching

Language: Python - Size: 10.8 MB - Last synced: 4 months ago - Pushed: 4 months ago - Stars: 34 - Forks: 7

FabrizioMusacchio/Napari_Bioimage_Analysis

Image data and Python scripts for the course on Bioimage analysis with Napari

Language: Python - Size: 46.4 MB - Last synced: 4 months ago - Pushed: 11 months ago - Stars: 2 - Forks: 0

antoineruzette/images-processing-made-easy

Encyclopedia of helper scripts to make 3D and 4D images processing easy.

Language: Jupyter Notebook - Size: 281 KB - Last synced: 9 months ago - Pushed: 9 months ago - Stars: 0 - Forks: 0

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

aberrations/Neurobiology-Fixtures-and-Microscopy-Tools

Simple devices and software to facilitate microscopy, electrophysiology, and microbiology techniques for systems neuroscience research. Easy to fabricate and use with low-cost 3D Printers.

Language: MATLAB - Size: 38.4 MB - Last synced: 10 months ago - Pushed: over 4 years ago - Stars: 0 - Forks: 0

Pablo1990/Bioimage_hackday_FIJIPlugin Fork of imagej/tutorials

Hackday project

Language: Java - Size: 76.7 MB - Last synced: 10 months ago - Pushed: almost 3 years ago - Stars: 0 - Forks: 1

WhoIsJack/tissue_exploder

Create a nice exploded visualization of segmented cells in a tissue.

Language: Python - Size: 12.2 MB - Last synced: 7 months ago - Pushed: 10 months ago - Stars: 4 - Forks: 1

josegcpa/wbs-prediction

Code repository for project focusing on blood cell detection and diagnostic prediction from peripheral blood slides

Language: R - Size: 81.1 MB - Last synced: 10 months ago - Pushed: 10 months ago - Stars: 1 - Forks: 1

leogolds/ConfluentFUCCI

A suite of tools for analyzing large scale confluent FUCCI experiments

Language: Python - Size: 121 MB - Last synced: 21 days ago - Pushed: about 2 months ago - Stars: 0 - Forks: 0

mahmoodlab/SISH

Fast and scalable search of whole-slide images via self-supervised deep learning - Nature Biomedical Engineering

Language: Python - Size: 958 KB - Last synced: 12 months ago - Pushed: 12 months ago - Stars: 72 - Forks: 22

chan-labsite/PCNAdeep

Track single cells and profile the cell cycle with PCNA fluorescence images

Language: Python - Size: 19 MB - Last synced: 9 months ago - Pushed: 9 months ago - Stars: 9 - Forks: 2

psobolewskiPhD/napari_scripts

Collection of useful (to me) python scripts for interacting with napari

Language: Python - Size: 47.9 KB - Last synced: about 1 month ago - Pushed: almost 2 years ago - Stars: 6 - Forks: 3

AlphonsG/BIMANA

Package for performing automated bio-image analysis tasks.

Language: Python - Size: 24.1 MB - Last synced: 4 months ago - Pushed: 7 months ago - Stars: 1 - Forks: 0

MontpellierRessourcesImagerie/napari-J

Connect Napari with FIJI/ImageJ

Language: Python - Size: 127 KB - Last synced: 29 days ago - Pushed: about 1 year ago - Stars: 3 - Forks: 2

Turku-BioImaging/split-and-merge

Fiji macro that splits and merges multi-dimensional TIFFs.

Language: ImageJ Macro - Size: 10.2 MB - Last synced: about 1 year ago - Pushed: over 1 year ago - Stars: 0 - Forks: 0

assafna/cell-ecm-project

Quantifying the dynamics of long-range cell-cell mechanical communication paper code

Language: Python - Size: 3.03 MB - Last synced: 10 months ago - Pushed: 10 months ago - Stars: 1 - Forks: 0

Altairch95/PICT-MODELLER

Scripts to estimate distances from PICT

Language: Python - Size: 167 MB - Last synced: about 1 year ago - Pushed: over 1 year ago - Stars: 0 - Forks: 0

FabrizioMusacchio/ZARR_tests

Python code that I used in my blog posts on the Zarr file format.

Language: Python - Size: 4.98 MB - Last synced: 4 months ago - Pushed: over 1 year ago - Stars: 0 - Forks: 0

MontpellierRessourcesImagerie/image-analysis-notebooks

Language: Jupyter Notebook - Size: 10.5 MB - Last synced: about 1 year ago - Pushed: almost 4 years ago - Stars: 3 - Forks: 0

danilexn/camos

CaMOS, a GUI for analysis of multimodal neuroscience datasets.

Language: Python - Size: 4.26 MB - Last synced: about 1 year ago - Pushed: over 2 years ago - Stars: 2 - Forks: 0

junelsolis/DeepSlides Fork of cialab/DeepSlides

cialab/DeepSlides fork to make it work with newer Python libraries.

Language: Python - Size: 17 MB - Last synced: about 1 year ago - Pushed: over 2 years ago - Stars: 0 - Forks: 0

chan-labsite/PCNAdeep-napari

Visualise pcnaDeep single-cell tracking data

Language: Python - Size: 748 KB - Last synced: about 1 year ago - Pushed: over 2 years ago - Stars: 2 - Forks: 2

AiviaCommunity/PythonQuickTips

Language: Python - Size: 4.34 MB - Last synced: about 1 year ago - Pushed: almost 4 years ago - Stars: 0 - Forks: 1

Vinit-source/CSL7382-Medical-image-clustering-assignment.py

The IPython notebook contains the questions as well as the related code. Only numpy has been used.

Language: Jupyter Notebook - Size: 1.51 MB - Last synced: about 1 year ago - Pushed: almost 3 years ago - Stars: 0 - Forks: 0

biomicrodev/jonaslab-cpp

Some CellProfiler plugins.

Language: Python - Size: 26.4 KB - Last synced: about 1 year ago - Pushed: about 3 years ago - Stars: 0 - Forks: 0

MontpellierRessourcesImagerie/mripy

MRI ImageJ related python (jython) module.

Language: Python - Size: 721 KB - Last synced: 4 months ago - Pushed: over 3 years ago - Stars: 1 - Forks: 0

ChasNelson1990/image-processing-in-python

This is the repository for an image-processing focussed self-taught course with a slight focus on bioimage analysis.

Language: Jupyter Notebook - Size: 2.04 MB - Last synced: 12 months ago - Pushed: almost 4 years ago - Stars: 0 - Forks: 1

miroslavradojevic/phdthesis

PhD dissertation: Methods for Automated Neuron Image Analysis candidate: Miroslav Radojevic Publisher: Erasmus University ISBN 978-94-6361-204-3

Language: TeX - Size: 278 MB - Last synced: about 1 year ago - Pushed: over 3 years ago - Stars: 1 - Forks: 0

fpBioImage/FPBioimageHelper-Icy

Language: Java - Size: 18.8 MB - Last synced: 2 months ago - Pushed: over 6 years ago - Stars: 0 - Forks: 0