cellfinder by brainglobe

Automated 3D cell detection in very large images

updated at May 20, 2024, 11:54 a.m.

15 +0

170 +0

38 +0

cloud-volume by seung-lab

Read and write Neuroglancer datasets programmatically.

updated at May 20, 2024, 1 p.m.

29 +1

126 +1

42 +0

TrackMate by trackmate-sc

TrackMate is your buddy for your everyday tracking.

updated at May 21, 2024, 3:48 a.m.

21 +0

148 +2

73 +0

FAST-Pathology by AICAN-Research

⚡ Open-source software for deep learning-based digital pathology

updated at May 21, 2024, 8:11 a.m.

7 +0

116 +1

23 +0

squidpy by scverse

Spatial Single Cell Analysis in Python

updated at May 21, 2024, 9:11 a.m.

9 +0

395 +2

71 +0

rivuletpy by RivuletStudio

Robust 3D Neuron Tracing / General 3D tree structure extraction in Python for 3D images powered by the Rivulet2 algorithm. Pain-free Install & use in 5 mins.

updated at May 21, 2024, 9:11 a.m.

7 +0

65 +1

17 +0

brainreg by brainglobe

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

updated at May 21, 2024, 12:13 p.m.

8 +0

111 -1

26 +0

root_painter by Abe404

RootPainter: Deep Learning Segmentation of Biological Images with Corrective Annotation

updated at May 21, 2024, 3:16 p.m.

5 +0

52 +1

11 +0

brainrender by brainglobe

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

updated at May 22, 2024, 1:52 a.m.

18 -1

513 +1

74 +0

pyImSegm by Borda

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

updated at May 22, 2024, 3:36 a.m.

14 +0

368 +2

73 +0

paquo by Bayer-Group

PAthological QUpath Obsession - QuPath and Python conversations

updated at May 22, 2024, 7:36 a.m.

10 +0

99 +2

16 +0

Usiigaci by oist

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

updated at May 22, 2024, 1:35 p.m.

14 +0

189 +1

70 +0

deepcell-tf by vanvalenlab

Deep Learning Library for Single Cell Analysis

updated at May 22, 2024, 5 p.m.

16 +0

392 +1

91 +0

CSBDeep by CSBDeep

Image restoration for fluorescence microscopy

updated at May 22, 2024, 5:33 p.m.

21 +0

266 +1

82 +1

spotiflow by weigertlab

Accurate and efficient spot detection for microscopy data

updated at May 22, 2024, 9:11 p.m.

3 +0

42 +1

4 +0

suite2p by MouseLand

cell detection in calcium imaging recordings

updated at May 22, 2024, 10:43 p.m.

18 +0

329 +1

236 +2

ThermImageJ by gtatters

ImageJ functions and macros for working with thermal image files

updated at May 23, 2024, 12:08 a.m.

8 +0

40 +1

6 +0

brainglobe-atlasapi by brainglobe

A lightweight python module to interact with atlases for systems neuroscience

updated at May 23, 2024, 8:10 a.m.

10 +0

113 +0

23 +0

fiji by fiji

A "batteries-included" distribution of ImageJ

updated at May 23, 2024, 3:28 p.m.

50 +0

717 +5

231 +0

n2v by juglab

This is the implementation of Noise2Void training.

updated at May 23, 2024, 5:41 p.m.

19 +0

376 +3

106 +1