bioimage-informatics

There are 1 repository under bioimage-informatics topic.

CLAM
mahmoodlab / CLAM
Open source tools for computational pathology - Nature BME
bioimage-informatics camelyon16 camelyon17 clam computational-pathology data-efficient deep-learning digital-pathology histopathology mahmoodlab pathology quantitative-pathology tcga-data weakly-supervised-learning whole-slide-imaging
Language:Python 1256
qupath / qupath
QuPath - Open-source bioimage analysis for research
bioimage-analysis bioimage-informatics cell-analysis cell-segmentation computational-pathology digital-pathology groovy histology image-processing imagej javafx machine-learning opencv pathology tissue-microarray-analysis whole-slide-imaging
Language:Java 1127
DigitalSlideArchive / HistomicsTK
A Python toolkit for pathology image analysis algorithms.
computer-vision medical-image-processing machine-learning bioimage-informatics histology python digital-slide-archive
Language:Python 411
mahmoodlab / CONCH
A vision-language foundation model for computational pathology - Nature Medicine
bioimage-analysis bioimage-informatics computational-pathology conch digital-pathology foundation-model health-informatics histopathology mahmoodlab medical-imaging nature-medicine nlp-machine-learning pathology quantitative-pathology vision-language-pathology
Language:Python 328
mahmoodlab / TOAD
AI-based pathology predicts origins for cancers of unknown primary - Nature
histology pathology wsi-images histopathology cancer-imaging-research cancer-research cancer-detection mahmoodlab deep deep-learning bioimage-analysis bioimage-informatics toad unknown-primary cup
Language:Python 171
DigitalSlideArchive / digital_slide_archive
The official deployment of the Digital Slide Archive and HistomicsTK.
histomicstk bioimage-informatics histology digital-slide-archive hacktoberfest
Language:Python 115
mahmoodlab / SISH
Fast and scalable search of whole-slide images via self-supervised deep learning - Nature Biomedical Engineering
bioimage-analysis bioimage-informatics deep-learning fish histology histopathology image-retrieval image-search-engine mahmoodlab pathology vqvae wsi-images
Language:Python 100
arttumiettinen / pi2
C++ library and command-line software for processing and analysis of terabyte-scale volume images locally or on a computing cluster.
3d-images bioimage-analysis bioimage-informatics bioimaging brain-imaging c-plus-plus cluster-computing computing-cluster cross-platform high-performance-computing image-analysis image-processing non-rigid-registration non-rigid-stitching python stitching tomography
Language:C++ 54
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 36
yu-lab-vt / SynQuant
A Fiji plugin that automatically quantify synapses from multi-channel fluorescence microscopy images.
bioimage-informatics fiji-plugin image-analysis synapse
Language:Java 14
joda01 / imagec
imageC / EVAnalyzer2 - High throughput biological image processor
biology image-processing science bioimage-analysis bioimage-informatics cell-segmentation opencv evanalyzer
Language:C++ 5
kumeS / BioImageDbs
Bio- and biomedical imaging dataset for machine learning and deep learning (for ExperimentHub in Bioconductor)
bioconductor bioimage bioimage-informatics experimenthub r
Language:HTML 2
murphygroup / docker-cellorganizer
CellOrganizer for Docker
cellorganizer docker virtualization container bioimage-informatics modelling
Language:Dockerfile 2
ghattab / seevis
SeeVIS is a (S)egmentation-fr(ee) (VIS)ualization pipeline for time-lapse image data. It comprises three steps: 1. preprocessing, 2. feature extraction, and 3. an extended version of the space time cube with three novel color mappings adapted to cell colony growth.
microfluidics time-series cell particle trajectory feature space visualization bioimage-informatics
Language:Python 1
ghattab / vicar
ViCAR extracts and employs (Vi)sual (C)ues for an (A)daptive (R)egistration of time-lapse image data recorded in microfluidic devices.
adaptive bioimage-informatics image landmark-free polygon registration
Language:Python 1
Jeff-Gui / PCNAdeep
Track single-cells and profile the cell cycle with PCNA images.
bioimage-informatics cell-biology cell-cycle
Language:Python 1
albagranados / cellviewer
Analysis of single molecule localization microscopy. 'pointpattern': statistical analysis. 'image': image processing+analysis+classification
r python bioimage-informatics
Language:Python 0
murphygroup / docker-cellorganizer-jupyter-notebook
CellOrganizer on Jupyter Notebook
cellorganizer docker virtualization container bioimage-informatics modeling
Language:Jupyter Notebook 0
murphygroup / singularity-cellorganizer
:whale: Script to build a Singularity image for CellOrganizer
cellorganizer container virtualization bioimage-informatics modeling-tools
Language:Shell 0
ghattab / cycasp
CYCASP is a methodology for investigating and understanding (C)olon(Y) growth and (C)ell (A)ttributes at the population level. It couples (SP)atiotemporal changes by relying on two novel data abstractions and a modular algorithm.
microfluidics time-series cell particle patch trajectory lineage abstraction dimensions feature bioimage-informatics
Language:Python
junelsolis / DeepSlides
cialab/DeepSlides fork to make it work with newer Python libraries.
pix2pix ki67 bioimage-informatics bioimage-analysis
Language:Python