Search Results - RepositoryStats

140

495

gpl-3.0

18

Code for the Nature Scientific Reports paper "Pathologist-level classification of histologic patterns on resected lung adenocarcinoma slides with deep neural networks." A sliding window framework for ...

wsi lung cancer resnet microscopy pathology-image sliding-windows histopathology-images medical-image-analysis

Created 2018-12-26

100 commits to master branch, last one 6 months ago

relion 3dem

203

457

gpl-2.0

50

Image-processing software for cryo-electron microscopy

Created 2017-01-26

7,141 commits to master branch, last one 11 days ago

pathml Dana-Farber-AIOS

83

400

gpl-2.0

13

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

1,384 commits to master branch, last one about a month ago

cucim rapidsai

61

362

apache-2.0

17

cuCIM - RAPIDS GPU-accelerated image processing library

gpu cuda nvidia image-data microscopy segmentation image-analysis computer-vision medical-imaging image-processing digital-pathology multidimensional-image-processing

Created 2021-04-09

544 commits to branch-25.02 branch, last one 10 days ago

pycroscopy pycroscopy

73

257

mit

32

Scientific analysis of nanoscale materials imaging data

Created 2016-06-18

4,051 commits to main branch, last one 18 days ago

CellViT TIO-IKIM

43

248

other

7

CellViT: Vision Transformers for Precise Cell Segmentation and Classification

ai ml cell python pytorch microscopy digitalpathology

Created 2023-06-20

94 commits to main branch, last one 6 months ago

pyclesperanto_prototype clEsperanto

46

215

bsd-3-clause

14

GPU-accelerated bio-image analysis focusing on 3D+t microscopy image data

microscopy gpu-acceleration bioimage-analysis

Created 2020-03-18

1,854 commits to master branch, last one 2 months ago

aicsimageio AllenCellModeling

51

207

other

10

Image Reading, Metadata Conversion, and Image Writing for Microscopy Images in Python

dask python xarray imageio microscopy bio-formats image-metadata scientific-formats scientific-computing

Created 2019-06-27

565 commits to main branch, last one 4 months ago

atomai pycroscopy

41

197

mit

11

Deep and Machine Learning for Microscopy

imaging pytorch materials microscopy deep-learning jupyter-notebook machine-learning ensemble-learning materials-science electron-microscopy google-colaboratory deep-kernel-learning multivariate-analysis semantic-segmentation variational-autoencoders scanning-probe-microscopy fully-convolutional-networks

Created 2020-09-04

1,412 commits to master branch, last one 10 months ago

cellfinder brainglobe

39

181

bsd-3-clause

15

Automated 3D cell detection in very large images

python imaging microscopy neuroanatomy neuroscience deep-learning cell-detection image-analysis

Created 2020-01-17

752 commits to main branch, last one 18 days ago

pytorch_connectomics zudi-lin

77

172

mit

6

PyTorch Connectomics: segmentation toolbox for EM connectomics

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

Created 2019-03-27

1,027 commits to master branch, last one 5 days ago

cloud-volume seung-lab

48

135

bsd-3-clause

29

Read and write Neuroglancer datasets programmatically.

Created 2017-07-25

1,337 commits to master branch, last one 2 days ago

webknossos scalableminds

24

131

agpl-3.0

15

Visualize, share and annotate your large 3D images online

em microscopy connectomics neurobiology hacktoberfest reconstruction microscopy-images

Created 2012-05-14

17,339 commits to master branch, last one 2 days ago

OAD zeiss-microscopy

51

129

gpl-3.0

19

Collection of tools and scripts useful to automate microscopy workflows in ZEN Blue using Python and Open Application Development tools and AI tools.

oad zen python imaging workflow zen-blue scripting automation microscopy acquisition open-source python-script image-analysis image-processing machine-learning

Created 2018-10-27

468 commits to master branch, last one 15 days ago

brainglobe-atlasapi brainglobe

34

128

bsd-3-clause

9

A Python interface to access neuroanatomical atlases

brain python atlases microscopy neuroscience registration visualisation

Created 2020-04-30

323 commits to main branch, last one 8 days ago

awesome-biological-image-analysis hallvaaw

24

127

cc0-1.0

5

A curated list of software, tools, pipelines, plugins etc. for image analysis related to biological questions.

imagej awesome biology imaging microscopy awesome-list cellprofiler segmentation image-analysis image-processing bioimage-analysis

Created 2022-03-20

133 commits to main branch, last one 2 months ago

brainreg brainglobe

29

124

bsd-3-clause

9

Automated 3D brain registration with support for multiple species and atlases.

brain atlases microscopy neuroanatomy neuroscience registration

Created 2020-05-26

221 commits to main branch, last one 18 days ago

axondeepseg axondeepseg

32

115

mit

13

Axon/Myelin segmentation using Deep Learning

axon myelin histology neuropoly microscopy spinalcord segmentation deep-learning machine-learning electron-microscopy convolutional-neural-networks

Created 2016-09-26

775 commits to master branch, last one a day ago

picasso jungmannlab

52

110

mit

16

A collection of tools for painting super-resolution images

smlm dna-paint microscopy super-resolution

Created 2016-10-27

2,374 commits to master branch, last one 7 days ago

MicroscopyNodes oanegros

8

102

gpl-3.0

5

Loading and handling microscopy data in blender

blender microscopy blender-addon volume-rendering

Created 2023-10-03

282 commits to main branch, last one 29 days ago

DECODE TuragaLab

26

96

gpl-3.0

7

This is the official implementation of our publication "Deep learning enables fast and dense single-molecule localization with high accuracy" (Nature Methods)

gpu smlm pytorch microscopy high-density deep-learning localization-microscopy

Created 2020-08-06

1,489 commits to master branch, last one about a year ago

cellseg_models.pytorch okunator

4

85

mit

2

Encoder-Decoder Cell and Nuclei segmentation models

ai ml timm pytorch cellpose hovernet omnipose stardist accelerate microscopy cell-segmentation digital-pathology pytorch-lightning nuclei-segmentation tissue-segmentation panoptic-segmentation

Created 2022-01-22

344 commits to main branch, last one 5 months ago

fold_slice yijiang1

27

85

unknown

12

Electron/X-ray ptychography and tomography/laminography

gpt microscopy tomography ptychography xray-diffraction computational-science

Created 2021-01-08

344 commits to main branch, last one 28 days ago

pycytominer cytomining

36

83

bsd-3-clause

6

Python package for processing image-based profiling data

python way-lab cytominer microscopy cellprofiler carpenter-lab image-processing morphological-profiling

Created 2019-07-03

754 commits to main branch, last one 9 days ago

Sparse-SIM WeisongZhao

13

77

odbl-1.0

4

Official MATLAB implementation of the "Sparse deconvolution" -v1.0.3

matlab-gui microscopy deconvolution image-processing super-resolution image-restoration fluorescence-microscopy-imaging

Created 2020-02-03

71 commits to master branch, last one 10 months ago

cytoself royerlab

14

74

bsd-3-clause

5

Self-supervised models for encoding protein localization patterns from microscopy images

imaging protein pytorch opencell microscopy tensorflow autoencoder fluorescence deep-learning self-supervised self-supervised-learning

Created 2021-04-27

88 commits to main branch, last one 3 months ago

pyotf david-hoffman

14

72

apache-2.0

7

python functions for simulating optical transfer functions

numpy microscopy

Created 2016-09-21

258 commits to master branch, last one 8 months ago

SUPPORT NICALab

16

72

gpl-3.0

6

Accurate denoising of voltage imaging data through statistically unbiased prediction, Nature Methods.

denoising microscopy deep-learning neural-network calcium-imaging voltage-imaging structural-imaging time-lapse-imaging self-supervised-learning

Created 2022-11-15

107 commits to main branch, last one 6 months ago

ImSwitch ImSwitch

53

71

gpl-3.0

9

ImSwitch is a software solution in Python that aims at generalizing microscope control by providing a solution for flexible control of multiple microscope modalities.

microscopy fluorescence super-resolution

Created 2020-03-20

3,063 commits to master branch, last one about a month ago

PlanktoScope PlanktoScope

25

67

cc-by-sa-4.0

6

Open and Affordable Quantitative Imaging Platform

ocean water citizen imaging science plankton microscope microscopy oceanography planktoscope raspberry-pi-4 citizen-science microscope-platform raspberry-pi-camera

Created 2020-03-19

879 commits to master branch, last one a day ago