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.

Python

10 +0

400 +2

86 +0

GitHub
pathml by Dana-Farber-AIOS

Tools for computational pathology

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

Python

13 +0

392 +0

84 +0

GitHub
CSBDeep by CSBDeep

Image restoration for fluorescence microscopy

created at June 5, 2018, 3:03 p.m.

Python

21 +0

284 +1

82 +0

GitHub
squidpy by scverse

Spatial Single Cell Analysis in Python

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

Python

9 +0

440 +4

79 +0

GitHub
brainrender by brainglobe

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

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

Python

17 +0

547 +3

77 +0

GitHub
pytorch_connectomics by zudi-lin

PyTorch Connectomics: segmentation toolbox for EM connectomics

created at March 27, 2019, 4:13 p.m.

Python

6 +0

172 +0

77 +0

GitHub
TrackMate by trackmate-sc

TrackMate is your buddy for your everyday tracking.

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

Java

20 +0

165 +1

75 +0

GitHub
pyImSegm by Borda

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

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

Python

14 +0

373 +0

73 +0

GitHub
CellProfiler-Analyst by CellProfiler

Open-source software for exploring and analyzing large, high-dimensional image-derived data.

created at Nov. 10, 2011, 6:57 p.m.

Python

21 +0

145 +0

72 +0

GitHub
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.

Jupyter Notebook

13 +0

193 +0

68 +0

GitHub
neurite by adalca

Neural networks toolbox focused on medical image analysis

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

Python

21 +0

339 +1

67 +1

GitHub
CaPTk by CBICA

Cancer Imaging Phenomics Toolkit (CaPTk) is a software platform to perform image analysis and predictive modeling tasks. Documentation: https://cbica.github.io/CaPTk

created at April 10, 2018, 1:36 p.m.

C++

5 +0

180 +0

64 +0

GitHub
Trainable_Segmentation by fiji

Fiji library to perform image segmentation based on the Weka learning schemes

created at April 3, 2014, 2:52 p.m.

Java

23 +0

112 +0

61 +0

GitHub
picasso by jungmannlab

A collection of tools for painting super-resolution images

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

Python

16 +0

110 +0

52 +0

GitHub
aicsimageio by AllenCellModeling

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

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

Python

10 +0

204 +0

51 +0

GitHub
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.

Jupyter Notebook

18 +0

127 +0

50 +0

GitHub
MorphoLibJ by ijpb

Collection of mathematical morphology methods and plugins for ImageJ

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

Java

17 +0

101 +0

48 +0

GitHub
cloud-volume by seung-lab

Read and write Neuroglancer datasets programmatically.

created at July 25, 2017, 5:34 p.m.

Python

29 +0

135 +3

47 +0

GitHub
micro-sam by computational-cell-analytics

Segment Anything for Microscopy

created at May 3, 2023, 11:36 a.m.

Jupyter Notebook

7 +0

360 +1

43 +0

GitHub
wholebrain by tractatus

R package for segmentation, registration and generating web-based brain atlases from microscope images

created at Oct. 29, 2015, 5:43 p.m.

C++

9 +0

85 +2

42 +0

GitHub