GitHub topics: bioimage-analysis
MercaderLabAnatomy/T-MIDAS
Automated batch processing for tissue microscopy image data
Language: Cool - Size: 35.9 MB - Last synced at: about 1 hour ago - Pushed at: about 2 hours ago - Stars: 6 - Forks: 1
sashielvagus/Preparing-Undergraduates-Through-Mentoring-towards-PHD-s-Project
Created two MATLAB codes using ROI and image-based processing to quantify the area of proliferation cells in three different types of tissues for numerous piglet uteri. Automated quantification of proliferating cell area, reducing analysis time from days to hours for biologists. Used image J for image analysis.
Language: MATLAB - Size: 3.42 MB - Last synced at: about 19 hours ago - Pushed at: about 20 hours ago - Stars: 0 - Forks: 0
danihae/bio-image-unet
Implementation of U-Net, U-Net++, and 3D U-Net in PyTorch for analysis of bio-images
Language: Python - Size: 248 KB - Last synced at: 3 days ago - Pushed at: 3 days ago - Stars: 5 - Forks: 0
qupath/qupath
QuPath - Open-source bioimage analysis for research
Language: Java - Size: 97.4 MB - Last synced at: 3 days ago - Pushed at: 3 days ago - Stars: 1,149 - Forks: 298
danihae/SarcAsM
A Python package for AI-based comprehensive analysis of sarcomere structure and function in cardiomyocytes
Language: Python - Size: 522 MB - Last synced at: 5 days ago - Pushed at: 5 days ago - Stars: 0 - Forks: 0
mahmoodlab/CONCH
Vision-Language Pathology Foundation Model - Nature Medicine
Language: Python - Size: 1.22 MB - Last synced at: 6 days ago - Pushed at: about 2 months ago - Stars: 355 - Forks: 28
kreshuklab/plant-seg
A tool for cell instance aware segmentation in densely packed 3D volumetric images
Language: Python - Size: 178 MB - Last synced at: 5 days ago - Pushed at: 6 days ago - Stars: 111 - Forks: 35
hallvaaw/awesome-biological-image-analysis
A curated list of software, tools, pipelines, plugins etc. for image analysis related to biological questions.
Size: 455 KB - Last synced at: 6 days ago - Pushed at: 2 months ago - Stars: 145 - Forks: 25
ArghaSarker/projection_upsampling_network
This is the repository for PU-Net, which is a deep learning based SIM reconstruction network for Structural Illumination Microscopy noisy image data.
Language: Python - Size: 388 MB - Last synced at: 8 days ago - Pushed at: 8 days ago - Stars: 0 - Forks: 0
ArghaSarker/RDL_denoising
Denoising Microscopy images with prior knowledge of Morier Patterns.
Language: Python - Size: 790 MB - Last synced at: 8 days ago - Pushed at: 8 days ago - Stars: 0 - Forks: 0
4DNucleome/PartSeg
Tool for segmentation in bioimaging
Language: Python - Size: 32.7 MB - Last synced at: 5 days ago - Pushed at: 7 days ago - Stars: 31 - Forks: 11
joda01/imagec
imageC / EVAnalyzer2 - High throughput biological image processor
Language: C++ - Size: 705 MB - Last synced at: 8 days ago - Pushed at: 8 days ago - Stars: 4 - Forks: 1
stardist/stardist
StarDist - Object Detection with Star-convex Shapes
Language: Python - Size: 114 MB - Last synced at: 7 days ago - Pushed at: 7 months ago - Stars: 1,026 - Forks: 240
MontpellierRessourcesImagerie/imagej_macros_and_scripts
ImageJ macros and scripts written at the imaging facility MRI
Language: Jupyter Notebook - Size: 17.1 MB - Last synced at: 12 days ago - Pushed at: 12 days ago - Stars: 33 - Forks: 17
SciCompJ/Imago
Generic Image processing Graphical application based on CS4J
Language: Java - Size: 5.61 MB - Last synced at: 13 days ago - Pushed at: 13 days ago - Stars: 0 - Forks: 0
mehta-lab/VisCy
computer vision models for single-cell phenotyping
Language: Python - Size: 33.4 MB - Last synced at: 6 days ago - Pushed at: 6 days ago - Stars: 46 - Forks: 4
mahmoodlab/SISH
Fast and scalable search of whole-slide images via self-supervised deep learning - Nature Biomedical Engineering
Language: Python - Size: 963 KB - Last synced at: 14 days ago - Pushed at: almost 2 years ago - Stars: 102 - Forks: 27
VeraPancaldiLab/tysserand
Fast reconstruction of spatial networks from bioimages.
Language: Python - Size: 68.8 MB - Last synced at: 17 days ago - Pushed at: 17 days ago - Stars: 25 - Forks: 6
kreshuklab/go-nuclear
Guides and code for 3D nuclear instance segmentation
Language: Python - Size: 687 KB - Last synced at: 19 days ago - Pushed at: 20 days ago - Stars: 22 - Forks: 3
mastodon-sc/mastodon
Mastodon – a large-scale tracking and track-editing framework for large, multi-view images.
Language: Java - Size: 23.1 MB - Last synced at: 18 days ago - Pushed at: 18 days ago - Stars: 73 - Forks: 20
clEsperanto/pyclesperanto_prototype
GPU-accelerated bio-image analysis focusing on 3D+t microscopy image data
Language: Jupyter Notebook - Size: 221 MB - Last synced at: 20 days ago - Pushed at: 3 months ago - Stars: 223 - Forks: 48
carpentries-incubator/bioimage-analysis-python
Bioimage Analysis with Python
Language: HTML - Size: 161 MB - Last synced at: 13 days ago - Pushed at: 14 days ago - Stars: 6 - Forks: 2
psobolewskiPhD/napari_scripts
Collection of useful (to me) python scripts for interacting with napari
Language: Python - Size: 47.9 KB - Last synced at: 28 days ago - Pushed at: over 2 years ago - Stars: 8 - Forks: 3
matjesg/deepflash2
A deep-learning pipeline for segmentation of ambiguous microscopic images.
Language: Jupyter Notebook - Size: 205 MB - Last synced at: 29 days ago - Pushed at: 7 months ago - Stars: 59 - Forks: 11
bioimage-io/core-bioimage-io-python
Python libraries for loading, running and packaging bioimage.io models
Language: Jupyter Notebook - Size: 10.4 MB - Last synced at: 10 days ago - Pushed at: about 1 month ago - Stars: 31 - Forks: 22
mahmoodlab/TOAD
AI-based pathology predicts origins for cancers of unknown primary - Nature
Language: Python - Size: 2.79 MB - Last synced at: about 1 month ago - Pushed at: over 3 years ago - Stars: 172 - Forks: 49
pertzlab/ARCOS-tutorial
A Jupyter notebook to identify collective cell signalling in raw microscopy images
Language: Jupyter Notebook - Size: 7.87 MB - Last synced at: 4 days ago - Pushed at: about 2 months ago - Stars: 1 - Forks: 1
romlambert/CytotoxPred
RF models for the prediction of cell viability in muscle cells from Cell Painting profiles.
Language: Jupyter Notebook - Size: 12.8 MB - Last synced at: about 2 months ago - Pushed at: about 2 months 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 at: about 1 month ago - Pushed at: about 2 months ago - Stars: 35 - Forks: 8
jhnnsrs/faser
A python based toolkit for psf estimation using a vectorial model of the electromagnetic field
Language: Python - Size: 16.3 MB - Last synced at: about 21 hours ago - Pushed at: 5 months ago - Stars: 3 - Forks: 0
miura/Yodosha-BIASBook2025
『型で実践する生物画像解析 ImageJ・Python・napari』サポートサイト
Language: Jupyter Notebook - Size: 51.1 MB - Last synced at: 2 months ago - Pushed at: 2 months ago - Stars: 0 - Forks: 0
haesleinhuepf/human-eval-bia
Benchmarking Large Language Models for Bio-Image Analysis Code Generation
Language: Jupyter Notebook - Size: 122 MB - Last synced at: 12 days ago - Pushed at: 6 months ago - Stars: 23 - Forks: 14
sanderslab/magellanmapper
MagellanMapper is a graphical interface for 3D bioimage annotation, atlas registration, and regional quantification
Language: Python - Size: 8.5 MB - Last synced at: 26 days ago - Pushed at: about 1 month ago - Stars: 21 - Forks: 4
tix209/TSOAX
Extraction and tracking of dynamic biopolymer networks.
Language: C++ - Size: 675 KB - Last synced at: 3 months ago - Pushed at: 3 months ago - Stars: 4 - Forks: 3
rgomez-AI/CellOrientation
Test of Uniformity for centrosome orientation at early timepoints during Wound Healing Assay
Language: R - Size: 929 KB - Last synced at: 3 months ago - Pushed at: 3 months ago - Stars: 0 - Forks: 0
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: 4.85 MB - Last synced at: about 2 months ago - Pushed at: about 2 months ago - Stars: 54 - Forks: 14
Oftatkofta/Oftatkofta.github.io
Landing page for my consulting compant
Language: HTML - Size: 25.1 MB - Last synced at: 7 months ago - Pushed at: 7 months ago - Stars: 0 - Forks: 0
rgomez-AI/3DChromTrans
Measure distances between two types of markers during FISH Assay after Chromosomal Translocation event
Language: Python - Size: 1.04 MB - Last synced at: 8 months ago - Pushed at: 8 months ago - Stars: 0 - Forks: 0
MontpellierRessourcesImagerie/napari-J
Connect Napari with FIJI/ImageJ
Language: Python - Size: 130 KB - Last synced at: 27 days ago - Pushed at: 9 months ago - Stars: 2 - Forks: 2
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 at: 2 months ago - Pushed at: almost 2 years ago - Stars: 3 - Forks: 0
leogolds/ConfluentFUCCI
A suite of tools for analyzing large scale confluent FUCCI experiments
Language: Python - Size: 121 MB - Last synced at: 4 days ago - Pushed at: 10 months ago - Stars: 0 - Forks: 0
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 at: 3 days ago - Pushed at: 12 months ago - Stars: 7 - 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
dl4mia/DL4MIA_2024
Main repository gathering all content of the EMBO-DL4MIA 2024 course.
Language: Shell - Size: 32.2 KB - Last synced at: about 1 year ago - Pushed at: about 1 year ago - Stars: 1 - Forks: 1
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 at: about 1 year ago - Pushed at: about 1 year ago - Stars: 0 - 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 at: about 1 year ago - Pushed at: about 1 year ago - Stars: 0 - Forks: 0
ai4life-opencalls/oc-1-project-6
Open Call #1: Murine Skeletal Muscle Analysis
Size: 37.4 MB - Last synced at: 10 months ago - Pushed at: about 1 year ago - Stars: 0 - Forks: 0
WhoIsJack/tissue_exploder
Create a nice exploded visualization of segmented cells in a tissue.
Language: Python - Size: 12.2 MB - Last synced at: 11 months ago - Pushed at: almost 2 years ago - Stars: 5 - Forks: 1
SOCR/3d-cell-morphometry
Source code and workflow protocols for SOCR 3D Cell Morphometry Project
Language: C - Size: 1.02 MB - Last synced at: about 1 year ago - Pushed at: almost 3 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 at: over 1 year ago - Pushed at: over 1 year ago - Stars: 2 - Forks: 0
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 at: over 1 year ago - Pushed at: about 5 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 at: over 1 year ago - Pushed at: over 6 years ago - Stars: 0 - 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 at: over 1 year ago - Pushed at: over 1 year 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 at: over 1 year ago - Pushed at: almost 2 years 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 at: almost 2 years ago - Pushed at: over 5 years ago - Stars: 0 - Forks: 0
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 at: almost 2 years ago - Pushed at: almost 2 years ago - Stars: 1 - Forks: 1
chan-labsite/PCNAdeep
Track single cells and profile the cell cycle with PCNA fluorescence images
Language: Python - Size: 19 MB - Last synced at: over 1 year ago - Pushed at: over 1 year ago - Stars: 9 - Forks: 2
Altairch95/PICT-MODELLER
Scripts to estimate distances from PICT
Language: Python - Size: 167 MB - Last synced at: 3 months ago - Pushed at: over 2 years ago - Stars: 0 - Forks: 0
AlphonsG/BIMANA
Package for performing automated bio-image analysis tasks.
Language: Python - Size: 24.1 MB - Last synced at: about 1 month ago - Pushed at: over 1 year ago - Stars: 1 - Forks: 0
Turku-BioImaging/split-and-merge
Fiji macro that splits and merges multi-dimensional TIFFs.
Language: ImageJ Macro - Size: 10.2 MB - Last synced at: about 2 years ago - Pushed at: over 2 years 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 at: almost 2 years ago - Pushed at: almost 2 years ago - Stars: 1 - 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 at: 2 months ago - Pushed at: over 2 years ago - Stars: 0 - Forks: 0
MontpellierRessourcesImagerie/image-analysis-notebooks
Language: Jupyter Notebook - Size: 10.5 MB - Last synced at: 6 months ago - Pushed at: almost 5 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 at: about 2 years ago - Pushed at: about 3 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 at: about 2 years ago - Pushed at: over 3 years ago - Stars: 0 - Forks: 0
chan-labsite/PCNAdeep-napari
Visualise pcnaDeep single-cell tracking data
Language: Python - Size: 748 KB - Last synced at: about 2 years ago - Pushed at: over 3 years ago - Stars: 2 - Forks: 2
AiviaCommunity/PythonQuickTips
Language: Python - Size: 4.34 MB - Last synced at: about 2 years ago - Pushed at: almost 5 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 at: about 2 months ago - Pushed at: almost 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 at: 7 months ago - Pushed at: almost 4 years ago - Stars: 0 - Forks: 1
biomicrodev/jonaslab-cpp
Some CellProfiler plugins.
Language: Python - Size: 26.4 KB - Last synced at: about 2 years ago - Pushed at: almost 4 years ago - Stars: 0 - Forks: 0
MontpellierRessourcesImagerie/mripy
MRI ImageJ related python (jython) module.
Language: Python - Size: 721 KB - Last synced at: 6 months ago - Pushed at: over 4 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 at: almost 2 years ago - Pushed at: almost 5 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 at: almost 2 years ago - Pushed at: over 4 years ago - Stars: 1 - Forks: 0
fpBioImage/FPBioimageHelper-Icy
Language: Java - Size: 18.8 MB - Last synced at: about 1 year ago - Pushed at: over 7 years ago - Stars: 0 - Forks: 0
