squidpy by scverse

Spatial Single Cell Analysis in Python

created at Aug. 21, 2020, 3:46 p.m.

9 +0

400 +0

70 -1

SMAP by jries

None

created at Nov. 2, 2018, 2:47 p.m.

9 +0

61 +0

20 +0

brainglobe-atlasapi by brainglobe

A lightweight python module to interact with atlases for systems neuroscience

created at April 30, 2020, 11:10 a.m.

10 +0

117 +1

24 +1

ark-analysis by angelolab

Integrated pipeline for multiplexed image analysis

created at Jan. 7, 2019, 4:31 a.m.

10 +0

67 +0

24 +0

image-quality by ocampor

Image quality is an open source software library for Image Quality Assessment (IQA).

created at July 6, 2019, 4:28 p.m.

10 +0

383 +0

84 +0

aicsimageio by AllenCellModeling

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

created at June 27, 2019, 4:43 p.m.

10 +0

196 +0

51 +0

paquo by Bayer-Group

PAthological QUpath Obsession - QuPath and Python conversations

created at July 6, 2020, 12:21 p.m.

10 +0

100 +0

16 +0

atomai by pycroscopy

Deep and Machine Learning for Microscopy

created at Sept. 4, 2020, 6:08 a.m.

11 +0

183 +1

39 +0

pathml by Dana-Farber-AIOS

Tools for computational pathology

created at July 31, 2019, 2:30 p.m.

12 +0

370 +0

81 +0

RS-FISH by PreibischLab

Tool for precise, interactive, fast and scalable FISH spot detection

created at Oct. 4, 2017, 5:01 p.m.

12 +0

45 +0

13 +0

minerva-story by labsyspharm

Minerva Story is an image viewer that is designed specifically to make it easy for non-expert users to interact with complex tissue images.

created at Dec. 16, 2019, 7:39 p.m.

12 +0

49 +0

14 +0

axondeepseg by axondeepseg

Axon/Myelin segmentation using Deep Learning

created at Sept. 26, 2016, 2:20 p.m.

13 +0

113 +0

32 +0

OpenMicroscopy by HohlbeinLab

Non-comprehensive list of projects and resources related to open microscopy.

created at Sept. 28, 2021, 8:51 a.m.

13 +0

124 +0

27 +0

Usiigaci by oist

Usiigaci: stain-free cell tracking in phase contrast microscopy enabled by supervised machine learning

created at June 15, 2018, 4:01 a.m.

13 -1

191 +0

68 +0

EBImage by aoles

Image processing toolbox for R

created at Aug. 15, 2014, 3:25 p.m.

13 +0

69 +1

28 +0

pyImSegm by Borda

Image segmentation - general superpixel segmentation & center detection & region growing

created at July 10, 2017, 2:17 a.m.

14 +0

368 +0

73 +0

picasso by jungmannlab

A collection of tools for painting super-resolution images

created at Oct. 27, 2016, 8:13 a.m.

15 +0

103 +1

48 +0

cellfinder by brainglobe

Automated 3D cell detection in very large images

created at Jan. 17, 2020, 2:14 p.m.

15 +0

172 +0

39 +0

nat by natverse

NeuroAnatomy Toolbox: An R package for the (3D) visualisation and analysis of biological image data, especially tracings of single neurons.

created at Jan. 2, 2014, 7:54 a.m.

17 +0

61 +0

26 +1

MorphoLibJ by ijpb

Collection of mathematical morphology methods and plugins for ImageJ

created at Feb. 10, 2014, 1:49 p.m.

17 +0

98 +1

49 +0