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The Top 23 Biomedical Image Processing Open Source Projects

Open source projects categorized as Biomedical Image Processing
Categories > Biomedical Image Processing
Pathml ⭐ 341
Tools for computational pathology
total releases 15most recent commit 4 months ago
Connected Components 3d ⭐ 289
Connected components on discrete and continuous multilabel 3D & 2D images. Handles 26, 18, and 6 connected variants.
dependent packages 18total releases 53most recent commit 6 months agopypi connected-components-3d} Downloads
Euclidean Distance Transform 3d ⭐ 201
Euclidean distance & signed distance transform for multi-label 3D anisotropic images using marching parabolas.
dependent packages 18total releases 35most recent commit 6 months agopypi edt} Downloads
Elektronn3 ⭐ 161
A PyTorch-based library for working with 3D and 2D convolutional neural networks, with focus on semantic segmentation of volumetric biomedical image data
dependent packages 1total releases 2most recent commit 6 months agopypi elektronn3} Downloads
Pytorch Unet ⭐ 154
Tunable U-Net implementation in PyTorch
most recent commit 4 years ago
Pytorch_connectomics ⭐ 151
PyTorch Connectomics: segmentation toolbox for EM connectomics
most recent commit 7 months ago
3dunet Tensorflow Brats18 ⭐ 147
3D Unet biomedical segmentation model powered by tensorpack with fast io speed
most recent commit 6 years ago
Pneumonia Detection From Chest X Ray Images With Deep Learning ⭐ 140
Detecting Pneumonia in Chest X-ray Images using Convolutional Neural Network and Pretrained Models
most recent commit 5 years ago
Gandlf ⭐ 127
A generalizable application framework for segmentation, regression, and classification using PyTorch
total releases 8most recent commit 4 months ago
Openeit ⭐ 127
Python based dashboard for real-time Electrical Impedance Tomography including image reconstruction using Back Projection, Graz Consensus and Gauss Newton methods
most recent commit 4 years ago
Visual Med Alpaca ⭐ 120
Visual Med-Alpaca is an open-source, multi-modal foundation model designed specifically for the biomedical domain, built on the LLaMa-7B.
most recent commit a year ago
Cloud Volume ⭐ 120
Read and write Neuroglancer datasets programmatically.
dependent packages 23total releases 319most recent commit 6 months agopypi cloud-volume} Downloads
Isic2018 ⭐ 113
ISIC 2018: Skin Lesion Analysis Towards Melanoma Detection
most recent commit 2 years ago
Kimimaro ⭐ 113
Skeletonize densely labeled 3D image segmentations with TEASAR. (Medial Axis Transform)
dependent packages 3total releases 48most recent commit 6 months agopypi kimimaro} Downloads
Ynet ⭐ 92
Y-Net: Joint Segmentation and Classification for Diagnosis of Breast Biopsy Images
most recent commit 3 years ago
Biapy ⭐ 85
Open source Python library for building bioimage analysis pipelines
most recent commit 4 months ago
Promise12_segmentation ⭐ 66
Codes that I have written to complete promise12 prostate segmentation competition.
most recent commit 6 years ago
Dijkstra3d ⭐ 60
Dijkstra's Shortest Path for 6, 18, and 26-Connected 3D (Volumetric) Image Volumes
dependent packages 1total releases 23most recent commit 6 months agopypi dijkstra3d} Downloads
Zmesh ⭐ 51
Marching Cubes & Mesh Simplification on multi-label 3D images.
dependent packages 3total releases 20most recent commit 7 months agopypi zmesh} Downloads
Sofima ⭐ 40
Scalable Optical Flow-based Image Montaging and Alignment
total releases 1most recent commit 5 months ago
Fastremap ⭐ 37
Remap, mask, renumber, unique, and in-place transposition of 3D labeled images. Point cloud too.
dependent packages 12total releases 36most recent commit 6 months agopypi fastremap} Downloads
Mmc ⭐ 33
Mesh-based Monte Carlo (MMC)
most recent commit 7 months ago
Skin Lesion Recognition.pytorch ⭐ 32
Rank3 Code for ISIC 2018: Skin Lesion Analysis Towards Melanoma Detection, Task 3
most recent commit 4 years ago
The 9 Most Depended On Biomedical Image Processing Open Source Projects
Cloud Volume ⭐ 120
Read and write Neuroglancer datasets programmatically.
dependent packages 23total releases 319latest release October 19, 2023most recent commit 6 months agopypi cloud-volume} Downloads
Connected Components 3d ⭐ 289
Connected components on discrete and continuous multilabel 3D & 2D images. Handles 26, 18, and 6 connected variants.
dependent packages 18total releases 53latest release August 26, 2023most recent commit 6 months agopypi connected-components-3d} Downloads
Euclidean Distance Transform 3d ⭐ 201
Euclidean distance & signed distance transform for multi-label 3D anisotropic images using marching parabolas.
dependent packages 18total releases 35latest release December 19, 2023most recent commit 6 months agopypi edt} Downloads
Fastremap ⭐ 37
Remap, mask, renumber, unique, and in-place transposition of 3D labeled images. Point cloud too.
dependent packages 12total releases 36latest release August 30, 2023most recent commit 6 months agopypi fastremap} Downloads
Tinybrain ⭐ 8
Image pyramid generation for grayscale and segmentation image resize.
dependent packages 4total releases 16latest release August 27, 2022most recent commit 6 months agopypi tinybrain} Downloads
Zmesh ⭐ 51
Marching Cubes & Mesh Simplification on multi-label 3D images.
dependent packages 3total releases 20latest release November 02, 2023most recent commit 7 months agopypi zmesh} Downloads
Kimimaro ⭐ 113
Skeletonize densely labeled 3D image segmentations with TEASAR. (Medial Axis Transform)
dependent packages 3total releases 48latest release March 24, 2022most recent commit 6 months agopypi kimimaro} Downloads
Dijkstra3d ⭐ 60
Dijkstra's Shortest Path for 6, 18, and 26-Connected 3D (Volumetric) Image Volumes
dependent packages 1total releases 23latest release August 31, 2021most recent commit 6 months agopypi dijkstra3d} Downloads
The 10 Latest Releases In Biomedical Image Processing Open Source Projects
Euclidean Distance Transform 3d ⭐ 201
Euclidean distance & signed distance transform for multi-label 3D anisotropic images using marching parabolas.
dependent packages 18total releases 35latest release December 19, 2023most recent commit 6 months agopypi edt} Downloads
Zmesh ⭐ 51
Marching Cubes & Mesh Simplification on multi-label 3D images.
dependent packages 3total releases 20latest release November 02, 2023most recent commit 7 months agopypi zmesh} Downloads
Cloud Volume ⭐ 120
Read and write Neuroglancer datasets programmatically.
dependent packages 23total releases 319latest release October 19, 2023most recent commit 6 months agopypi cloud-volume} Downloads
Fastremap ⭐ 37
Remap, mask, renumber, unique, and in-place transposition of 3D labeled images. Point cloud too.
dependent packages 12total releases 36latest release August 30, 2023most recent commit 6 months agopypi fastremap} Downloads
Connected Components 3d ⭐ 289
Connected components on discrete and continuous multilabel 3D & 2D images. Handles 26, 18, and 6 connected variants.
dependent packages 18total releases 53latest release August 26, 2023most recent commit 6 months agopypi connected-components-3d} Downloads
Microviewer ⭐ 8
Multiplatform 3D numpy image browser based viewer with voxel painting.
total releases 13latest release July 05, 2023most recent commit a year ago
Pathml ⭐ 341
Tools for computational pathology
total releases 15latest release May 30, 2023most recent commit 4 months ago
Gandlf ⭐ 127
A generalizable application framework for segmentation, regression, and classification using PyTorch
total releases 8latest release September 20, 2022most recent commit 4 months ago
Tinybrain ⭐ 8
Image pyramid generation for grayscale and segmentation image resize.
dependent packages 4total releases 16latest release August 27, 2022most recent commit 6 months agopypi tinybrain} Downloads
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