neurite by adalca

Neural networks toolbox focused on medical image analysis

created at March 10, 2017, 1:25 a.m.

21 +0

324 +2

65 +0

TrackMate by trackmate-sc

TrackMate is your buddy for your everyday tracking.

created at Dec. 19, 2013, 8:01 p.m.

20 +0

152 +0

73 +0

n2v by juglab

This is the implementation of Noise2Void training.

created at Jan. 11, 2019, 5:43 p.m.

19 +0

382 +1

107 +0

thunderstorm by zitmen

ThunderSTORM: a comprehensive ImageJ plugin for SMLM data analysis and super-resolution imaging

created at May 3, 2015, 6:59 p.m.

18 +0

91 +1

42 -1

OAD by zeiss-microscopy

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

created at Oct. 27, 2018, 4:42 p.m.

18 +0

121 +0

47 +0

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

suite2p by MouseLand

cell detection in calcium imaging recordings

created at July 16, 2018, 6:12 p.m.

17 +0

329 +0

237 +0

deepslide by BMIRDS

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 classification of high resolution whole-slide images, often microscopy or histopathology images.

created at Dec. 26, 2018, 1:51 a.m.

17 +0

476 +0

136 +0

deepcell-tf by vanvalenlab

Deep Learning Library for Single Cell Analysis

created at May 16, 2018, 5:41 p.m.

17 +0

401 +1

91 +0

brainrender by brainglobe

a python based software for visualization of neuroanatomical and morphological data.

created at Sept. 19, 2019, 9:27 a.m.

17 -1

521 +0

75 +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

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

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

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

EBImage by aoles

Image processing toolbox for R

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

13 +0

69 +1

28 +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

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

axondeepseg by axondeepseg

Axon/Myelin segmentation using Deep Learning

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

13 +0

113 +0

32 +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

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