Search Results - RepositoryStats

84

419

gpl-2.0

11

Tools for computational pathology

pathml python pytorch research pathology microscopy deep-learning histopathology image-analysis machine-learning digital-pathology computational-pathology spatial-transcriptomics biomedical-image-processing fluorescence-microscopy-imaging

Created 2019-07-31

1,385 commits to master branch, last one 2 months ago

connected-components-3d seung-lab

46

411

lgpl-3.0

28

Connected components on discrete and continuous multilabel 3D & 2D images. Handles 26, 18, and 6 connected variants; periodic boundaries (4, 8, & 6)

Created 2018-08-28

449 commits to master branch, last one about a month ago

visual-med-alpaca cambridgeltl

42

383

apache-2.0

14

Visual Med-Alpaca is an open-source, multi-modal foundation model designed specifically for the biomedical domain, built on the LLaMa-7B.

biomedical multimodal foundation-model large-language-models biomedical-image-processing

Created 2023-04-11

61 commits to main branch, last one about a year ago

euclidean-distance-transform-3d seung-lab

36

248

lgpl-3.0

24

Euclidean distance & signed distance transform for multi-label 3D anisotropic images using marching parabolas.

1d 2d 3d cpp numpy python parallel algorithm anisotropy anisotropic connectomics neuroscience distance-transform euclidean-distance marching-parabolas signed-distance-field signed-distance-functions biomedical-image-processing euclidean-distance-transform

Created 2018-07-25

224 commits to master branch, last one about a month ago

OpenEIT OpenEIT

73

232

other

27

Python based dashboard for real-time Electrical Impedance Tomography including image reconstruction using Back Projection, Graz Consensus and Gauss Newton methods

eit python tomography inverse-problems image-reconstruction biomedical-instrumentation biomedical-image-processing electrical-impedance-tomography

Created 2017-11-22

156 commits to master branch, last one 12 days ago

pytorch_connectomics zudi-lin

78

179

mit

5

PyTorch Connectomics: segmentation toolbox for EM connectomics

pytorch microscopy connectomics neuroscience segmentation deep-learning computer-vision biomedical-image-processing

Created 2019-03-27

1,038 commits to master branch, last one 2 months ago

GaNDLF mlcommons

86

174

apache-2.0

7

A generalizable application framework for segmentation, regression, and classification using PyTorch

pytorch framework regression segmentation deep-learning classification medical-imaging machine-learning clinical-workflow data-augmentation medical-informatics medical-image-analysis biomedical-image-processing

Created 2021-02-26

9,719 commits to master branch, last one 13 days ago

elektronn3 ELEKTRONN

28

164

mit

16

A PyTorch-based library for working with 3D and 2D convolutional neural networks, with focus on semantic segmentation of volumetric biomedical image data

3d-cnn pytorch electron-microscopy semantic-segmentation 3d-convolutional-network biomedical-image-processing convolutional-neural-networks

Created 2017-12-11

988 commits to master branch, last one about a year ago

cloud-volume seung-lab

48

146

bsd-3-clause

30

Read and write Neuroglancer datasets programmatically.

Created 2017-07-25

1,370 commits to master branch, last one 4 days ago

kimimaro seung-lab

26

146

gpl-3.0

24

Skeletonize densely labeled 3D image segmentations with TEASAR. (Medial Axis Transform)

voxel python teasar skeletons centerline connectomics cross-section skeletonization volumetric-data cross-section-area image-segmentation centerline-extraction medial-axis-transform computer-vision-algorithms biomedical-image-processing

Created 2019-01-16

291 commits to master branch, last one about a month ago

BiaPy BiaPyX

30

144

mit

6

Open source Python library for building bioimage analysis pipelines

python pytorch denoising segmentation deep-learning classification computer-vision medical-imaging image-processing machine-learning object-detection super-resolution image-segmentation instance-segmentation semantic-segmentation self-supervised-learning biomedical-image-processing convolutional-neural-networks

Created 2019-02-28

2,258 commits to master branch, last one 3 days ago

ISIC2018 yuanqing811

51

141

unknown

6

ISIC 2018: Skin Lesion Analysis Towards Melanoma Detection

deep-learning computer-vision melanoma-recognition biomedical-image-processing

Created 2018-06-04

18 commits to master branch, last one 6 years ago

MRISkullStripping amrzhd

2

94

mit

1

Developing a UNet3D model for accurate MRI skull stripping using the Calgary Campinas 359 dataset, enhancing neuroimaging preprocessing workflows.

mri unet monai python nibabel pytorch mri-images image-segmentation unet-image-segmentation biomedical-image-processing

Created 2024-08-18

10 commits to main branch, last one 5 months ago

dijkstra3d seung-lab

14

79

gpl-3.0

21

Dijkstra's Shortest Path for 6, 18, and 26-Connected 3D (Volumetric) Image Volumes

2d 3d cpp a-star python dijkstra pathfinding a-star-search path-planning shortest-path skeletonization 3d-image-volumes a-star-algorithm dijkstra-algorithm bidirectional-search unidirectional-search bidirectional-dijkstra dijkstra-shortest-path biomedical-image-processing

Created 2018-08-02

228 commits to master branch, last one 3 months ago

sofima google-research

16

68

apache-2.0

7

Scalable Optical Flow-based Image Montaging and Alignment

2d 3d 4d jax python3 microscopy connectomics alignment-algorithm electron-microscopy stitching-algorithm biomedical-image-processing

Created 2022-02-11

82 commits to main branch, last one 2 months ago

OCT-Retinal-Layer-Segmenter beasygo1ng

7

67

unknown

3

UNet based model that segment retina to 8 layers in OCT images

images python segmentation deep-learning neural-networks keras-tensorflow machine-learning image-segmentation deep-neural-networks biomedical-data-science computer-vision-algorithms retinal-layer-segmentation biomedical-image-processing

Created 2022-06-20

18 commits to master branch, last one 2 years ago

zmesh seung-lab

8

62

gpl-3.0

19

Marching Cubes & Mesh Simplification on multi-label 3D images.

python meshing connectomics marching-cubes mesh-generation mesh-processing volumetric-data mesh-simplification marching-cubes-algorithm biomedical-image-processing

Created 2019-04-29

145 commits to master branch, last one about a month ago

im2im-uq aangelopoulos

9

55

mit

4

Image-to-image regression with uncertainty quantification in PyTorch. Take any dataset and train a model to regress images to images with rigorous, distribution-free uncertainty quantification.

mri unet pytorch microscopy uncertainty machine-learning quantile-regression computational-biology computational-imaging uncertainty-estimation biomedical-data-science image-to-image-translation uncertainty-quantification biomedical-image-processing

Created 2021-05-30

152 commits to main branch, last one 2 years ago

fastremap seung-lab

6

54

lgpl-3.0

16

Remap, mask, renumber, unique, and in-place transposition of 3D labeled images. Point cloud too.

numpy remap cython python unique looping masking python3 in-place remapping transpose point-cloud renumbering array-manipulations in-place-transposition biomedical-image-processing

Created 2019-01-16

171 commits to master branch, last one a day ago