bioimaging

There are 2 repositories under bioimaging topic.

ome / ngff
Next-generation file format (NGFF) specifications for storing bioimaging data in the cloud.
bioimaging spec file-formats cloud data-science
Language:Bikeshed 104
arttumiettinen / pi2
C++ library and command-line software for processing and analysis of terabyte-scale volume images locally or on a computing cluster.
image-analysis python 3d-images tomography image-processing brain-imaging c-plus-plus cluster-computing computing-cluster high-performance-computing stitching non-rigid-registration non-rigid-stitching cross-platform bioimaging bioimage-analysis bioimage-informatics
Language:C++ 48
chanzuckerberg / napari-hub
Discover, install, and share napari plugins
napari python bioimaging deep-learning machine-learning analysis imaging segmentation registration detection denoising themes plugins napari-plugin tracking
Language:TypeScript 48
ciccalab / SIMPLI
SIMPLI is a highly configurable pipeline for the analysis of multiplexed imaging data.
cell-segmentation single-cell-analysis imaging-mass-cytometry immunofluorescence histological-images gating tissue-analysis tissue-classification histology bioimage-analysis bioimaging bioimage-tools bioimage-informatics mcd imc life-sciences-image ome-tiff image-analysis-workflows
Language:R 33
BodenmillerGroup / cytomapper
R package for visualization of highly multiplexed imaging data
bioimaging imaging-mass-cytometry single-cell spatial-analysis
Language:R 32
czbiohub-sf / iohub
Pythonic and parallelizable I/O for N-dimensional imaging data with OME metadata
bioimaging image-metadata ndimensional-arrays python
Language:Python 26
bioimage-io / core-bioimage-io-python
Python libraries for loading, running and packaging bioimage.io models
bioimage-analysis bioimage-infomatics bioimaging deep-learning
Language:Jupyter Notebook 18
anthonytec2 / xrayscanner
Python 3 x-ray simulator
bioimaging detector gpu-computing imaging-scenario numba numpy python xray
Language:Jupyter Notebook 14
TileDB-Inc / TileDB-BioImaging
Package providing bioimaging functionality using TileDB. Source of the tiledb-bioimg Python package.
bioimaging python-package tiledb
Language:Python 14
NL-BioImaging / biomero
BIOMERO - A python library for easy connecting between OMERO (jobs) and a Slurm cluster
biaflows bioimaging biomero cytomine fair high-content-screening high-performance-computing high-throughput-screening image-analysis omero python slurm
Language:Python 12
rezacsedu / DeepCOVIDExplainer
DeepCOVIDExplainer: Explainable COVID-19 Diagnosis from Chest X-ray Images
artificial-intelligence deep-neural-networks deep-learning bioimaging bioinformatics healthcare covid-19
Language:Jupyter Notebook 11
TileDB-Inc / napari-tiledb-bioimg
TileDB BioImaging plugin for Napari
bioimaging napari napari-plugin tiledb
Language:Python 7
AlanRace / biquinho
Visualisation software for imaging mass cytometry data
bioimaging imaging-mass-cytometry visualization
Language:Rust 6
ggirelli / radiantkit
A Python3 Radial Image Analysis Toolkit
bioimaging microscopy image-analysis format-conversion-tool image-segmentation image-processing hacktoberfest
Language:Python 3
NL-BioImaging / biomero-scripts
Scripts for use with BIOMERO
biaflows bioimaging biomero cytomine fair high-content-screening high-performance-computing high-throughput-screening image-analysis omero slurm
Language:Python 3
molecular-partner-prediction
Yu-Group / molecular-partner-prediction
Predicting successful CME events using only clathrin markers. 🦠📈
bioimaging bioinformatics cell-biology cell-transport classification computational computational-biology data-science endocytosis feature-engineering machine-learning prediction python3 segmentation statistics tracking
Language:Jupyter Notebook 2
zarr-developers / zarr-developers.github.io
Zarr Homepage
bioimaging conventions format geospatial ndimensional-arrays zarr
Language:JavaScript 2
AlanRace / imc-rs
Rust library for reading imaging mass cytometry (IMC) data stored in .mcd files.
imaging-mass-cytometry rust bioimaging multiplexed-imaging
Language:Rust 1
aquilesC / background-free
Paper on how to supress background while imaging gold nanorods through the use of the anti-Stokes emission.
nanoparticles nanorods gold imaging anti-stokes luminescence bioimaging background-suppression
Language:TeX 1
SpectraScope
ggirelli / SpectraScope
Interactive interface to visualize spectra and filter sets for any microscope. Easily customizable.
spectrum spectra optics wavelength filter color microscopy microscope bioimaging
Language:JavaScript 1
ome / B3D
Clone of https://git.embl.de/balazs/B3D
bioimaging codec compression hdf5
Language:C++ 1
psobolewskiPhD / JAX_NEBioimaging_napari_community_slides
Slides for a presentation about contributing to the napari community
bioimaging napari
Language:HTML 1
chillxcode / Classification-of-Breast-Cancer-Images-Using-Deep-Learning-Methods
Graduation Project
bach bioimaging breast-cancer-images classification cnn keras
Language:Python 0
sule213 / anavo
Analysis of variance (ANOVA) is a collection of statistical models and their associated estimation procedures (such as the "variation" among and between groups) used to analyze the differences among means.
bioimaging bioinformatics-analysis bioinformatics-pipeline computer-vision image-processing scientific-computing
Language:Jupyter Notebook 0
Turku-BioImaging / omero-docker
Deploy an OMERO server using Docker Compose
bioimaging docker microscopy omero
Language:Shell 0
FabrizioMusacchio / ZARR_tests
Python code that I used in my blog posts on the Zarr file format.
ome omero python zarr bioimage-analysis bioimaging microscopy-data microscopy-images ome-zarr
Language:Python
ome / conda-omero-py
OMERO.py Conda package
ome omero conda python bioimaging py-conda
YogiOnBioinformatics / Bioimaging-Informatics-Machine-Learning-for-Cancerous-Breast-Cell-Detection
Worked with Dr. Shandong Wu at University of Pittsburgh to use software to improve outcomes for breast cancer risk detection.
bioimaging bioinformatics computational-biology machine-learning cancer-imaging-research matlab mammography-density breast-cancer breast-cancer-prediction breast-cancer-tumor breast-cancer-diagnosis prediction-algorithm fuzzy-cmeans-clustering support-vector-machines
Language:MATLAB
zarr-developers / blog
Zarr Official Blog
bioimaging blog data-format geospatial giscus zarr
Language:Ruby

bioimaging

ome / ngff

arttumiettinen / pi2

chanzuckerberg / napari-hub

ciccalab / SIMPLI

BodenmillerGroup / cytomapper

czbiohub-sf / iohub

bioimage-io / core-bioimage-io-python

anthonytec2 / xrayscanner

TileDB-Inc / TileDB-BioImaging

NL-BioImaging / biomero

rezacsedu / DeepCOVIDExplainer

TileDB-Inc / napari-tiledb-bioimg

AlanRace / biquinho

ggirelli / radiantkit

NL-BioImaging / biomero-scripts

Yu-Group / molecular-partner-prediction

zarr-developers / zarr-developers.github.io

AlanRace / imc-rs

aquilesC / background-free

ggirelli / SpectraScope

ome / B3D

psobolewskiPhD / JAX_NEBioimaging_napari_community_slides

chillxcode / Classification-of-Breast-Cancer-Images-Using-Deep-Learning-Methods

sule213 / anavo

Turku-BioImaging / omero-docker

FabrizioMusacchio / ZARR_tests

ome / conda-omero-py

YogiOnBioinformatics / Bioimaging-Informatics-Machine-Learning-for-Cancerous-Breast-Cell-Detection

zarr-developers / blog