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whole-slide-imaging

Here are 88 public repositories matching this topic...

CLAM

mahmoodlab / CLAM

Data-efficient and weakly supervised computational pathology on whole slide images - Nature Biomedical Engineering

deep-learning tcga-data weakly-supervised-learning bioimage-informatics digital-pathology clam pathology whole-slide-imaging computational-pathology camelyon16 histopathology camelyon17 data-efficient mahmoodlab quantitative-pathology

Updated Jul 31, 2024
Python

qupath / qupath

QuPath - Open-source bioimage analysis for research

groovy opencv machine-learning imagej javafx image-processing histology cell-segmentation bioimage-informatics digital-pathology pathology whole-slide-imaging cell-analysis computational-pathology bioimage-analysis tissue-microarray-analysis

Updated Nov 15, 2024
Java

baidu-research / NCRF

Cancer metastasis detection with neural conditional random field (NCRF)

deep-learning conditional-random-fields pathology whole-slide-imaging camelyon16

Updated Oct 3, 2023
Python

computationalpathologygroup / ASAP

Program for the analysis and visualization of whole-slide images in digital pathology

whole-slide-imaging computation-pathology

Updated Sep 12, 2023
C++

cgohlke / tifffile

Read and write TIFF files

python image imagej numpy tiff format-reader life-sciences-image ome-tiff whole-slide-imaging zarr

Updated Sep 20, 2024
Python

openslide / openslide

C library for reading virtual slide images

c pathology whole-slide-imaging

Updated Oct 30, 2024
C

TissueImageAnalytics / tiatoolbox

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

python machine-learning deep-learning image-analysis cell-segmentation digital-pathology whole-slide-imaging medical-image-analysis computational-pathology cell-classification histopathology stain-normalization tissue-segmentation tissue-analysis

Updated Nov 15, 2024
Python

ome / bioformats

Bio-Formats is a Java library for reading and writing data in life sciences image file formats. It is developed by the Open Microscopy Environment. Bio-Formats is released under the GNU General Public License (GPL); commercial licenses are available from Glencoe Software.

java metadata image format-reader format-converter bio-formats life-sciences-image whole-slide-imaging wsi lightsheet

Updated Nov 14, 2024
Java

binli123 / dsmil-wsi

DSMIL: Dual-stream multiple instance learning networks for tumor detection in Whole Slide Image

deep-neural-networks deep-learning pytorch transformer semi-supervised-learning weakly-supervised-learning whole-slide-imaging tumor-detection self-attention self-supervised-learning multiple-instance-learning histopathology whole-slide-image visiontransformer

Updated Apr 29, 2024
Python

slideflow

slideflow / slideflow

Powerful, open-source AI tools for digital pathology.

python machine-learning deep-learning histology pathology whole-slide-imaging computational-pathology histopathology

Updated Nov 14, 2024
Python

camicroscope / caMicroscope

Digital pathology image viewer with support for human/machine generated annotations and markups.

slide-images digital-pathology whole-slide-imaging camicroscope

Updated Nov 14, 2024
JavaScript

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]

Updated Oct 29, 2024
Python

MarvinLer / tcga_segmentation

Whole Slide Image segmentation with weakly supervised multiple instance learning on TCGA | MICCAI2020 https://arxiv.org/abs/2004.05024

tcga medical-imaging segmentation image-segmentation tcga-data weakly-supervised-learning miccai pathology whole-slide-imaging wsi computational-pathology multiple-instance-learning tumor-segmentation histopathology data-efficient slide-image-segmentation

Updated Aug 5, 2021
Python

cylab-tw / bluelight

a browser-based DICOM viewer

html5 dicom dicomweb bluelight dicom-server whole-slide-imaging dicom-viewer orthanc wsi rtss dicom-web-viewer dicom-overlay

Updated Oct 31, 2024
JavaScript

ChongQingNoSubway / PDL

Code for the paper " PDL: Regularizing Multiple Instance Learning with Progressive Dropout Layers "

weakly-supervised-learning whole-slide-imaging tumor-detection multiple-instance-learning histopathology histopathology-images whole-slide-image histopathology-image-analysis

Updated Jul 11, 2024
Python

ChongQingNoSubway / DGR-MIL

Code for paper: DGR-MIL: Exploring Diverse Global Representation in Multiple Instance Learning for Whole Slide Image Classification [ECCV 2024]

transformer weakly-supervised-learning whole-slide-imaging tumor-heterogeneity tumor-detection self-attention multiple-instance-learning tumor-classification histopathology histopathology-image-analysis

Updated Sep 21, 2024
Python

DIAGNijmegen / pathology-whole-slide-data

A package for working with whole-slide data including a fast batch iterator that can be used to train deep learning models.

python deep-learning iterator wsd pathology whole-slide-imaging wsi computational-pathology wsm wsa histopathology whole-slide-image whole-slide-annotation whole-slide-mask whole-slide-dataset whole-slide-data

Updated Nov 7, 2024
Python

btcrabb / SlideSeg

A Python module that produces image patches and annotation masks from whole slide images for deep learning in digital pathology.

convolutional-neural-networks semantic-segmentation digital-pathology whole-slide-imaging

Updated Jun 21, 2022
Jupyter Notebook

cytomine / Cytomine-core

Cytomine-Core is the main web server implementing the Cytomine API

machine-learning digital-pathology whole-slide-imaging computational-pathology cytomine

Updated Feb 24, 2023
Groovy

YashSharma / C2C

Implementation of Cluster-to-Conquer: A Framework for End-to-End Multi-Instance Learning for Whole Slide Image Classification approach.

deep-learning weakly-supervised-learning whole-slide-imaging multiple-instance-learning histopathology

Updated Oct 12, 2021
Python

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