n2v by juglab

This is the implementation of Noise2Void training.

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

19 +0

371 +1

106 +1

pathml by Dana-Farber-AIOS

Tools for computational pathology

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

12 +0

364 +2

78 +0

pyImSegm by Borda

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

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

14 +0

364 +0

74 +0

ilastik by ilastik

ilastik-shell, applets, and workflows to string them together.

created at May 8, 2012, 3:59 p.m.

41 +0

338 +1

130 +0

suite2p by MouseLand

cell detection in calcium imaging recordings

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

18 +0

327 +0

232 +0

neurite by adalca

Neural networks toolbox focused on medical image analysis

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

21 +0

317 +1

65 +0

micro-sam by computational-cell-analytics

Segment Anything for Microscopy

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

8 +1

293 +9

35 +0

CSBDeep by CSBDeep

Image restoration for fluorescence microscopy

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

21 +0

265 +1

80 +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

192 +0

50 +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.

14 +0

188 +0

70 +0

atomai by pycroscopy

Deep and Machine Learning for Microscopy

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

11 +0

181 +0

36 +0

cellfinder by brainglobe

Automated 3D cell detection in very large images

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

15 +0

170 +0

38 +0

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.

4 +0

169 +0

63 +0

pytorch_connectomics by zudi-lin

PyTorch Connectomics: segmentation toolbox for EM connectomics

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

6 +0

163 +0

74 +0

TrackMate by trackmate-sc

TrackMate is your buddy for your everyday tracking.

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

21 +0

143 +1

71 +1

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.

21 +0

140 +0

72 +0

cloud-volume by seung-lab

Read and write Neuroglancer datasets programmatically.

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

28 +0

125 +0

42 +0

OpenMicroscopy by HohlbeinLab

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

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

12 +0

120 +0

26 +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

119 +0

47 +0

Cell_ACDC by SchmollerLab

A Python GUI-based framework for segmentation, tracking and cell cycle annotations of microscopy data

created at Feb. 25, 2021, 4:14 p.m.

5 +0

117 +1

20 +0