napari by napari

napari: a fast, interactive, multi-dimensional image viewer for python

updated at June 2, 2024, 10:24 a.m.

48 +0

2,086 +9

411 +2

brainglobe-atlasapi by brainglobe

A lightweight python module to interact with atlases for systems neuroscience

updated at June 2, 2024, 7:02 a.m.

10 +0

114 +1

23 +0

brainrender by brainglobe

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

updated at June 2, 2024, 6:59 a.m.

18 +0

517 +4

75 +1

pytorch_connectomics by zudi-lin

PyTorch Connectomics: segmentation toolbox for EM connectomics

updated at June 2, 2024, 2:06 a.m.

6 +0

164 +1

74 +0

scikit-image by scikit-image

Image processing in Python

updated at June 1, 2024, 11:28 p.m.

186 +0

5,907 +6

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plant-seg by kreshuklab

A tool for cell instance aware segmentation in densely packed 3D volumetric images

updated at June 1, 2024, 9:32 p.m.

7 +0

86 +0

30 +0

atomai by pycroscopy

Deep and Machine Learning for Microscopy

updated at June 1, 2024, 7:47 a.m.

11 +0

182 +1

38 +0

CSBDeep by CSBDeep

Image restoration for fluorescence microscopy

updated at June 1, 2024, 1:22 a.m.

21 +0

267 +1

82 +0

squidpy by scverse

Spatial Single Cell Analysis in Python

updated at June 1, 2024, 12:41 a.m.

9 +0

399 +4

71 +0

CaImAn by flatironinstitute

Computational toolbox for large scale Calcium Imaging Analysis, including movie handling, motion correction, source extraction, spike deconvolution and result visualization.

updated at May 31, 2024, 7:26 p.m.

47 +0

610 +1

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picasso by jungmannlab

A collection of tools for painting super-resolution images

updated at May 31, 2024, 3:47 p.m.

16 +0

102 +2

48 +1

Cell_ACDC by SchmollerLab

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

updated at May 31, 2024, 1:22 p.m.

5 +0

119 +1

20 +0

n2v by juglab

This is the implementation of Noise2Void training.

updated at May 31, 2024, 9:12 a.m.

19 +0

378 +2

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plantcv by danforthcenter

Plant phenotyping with image analysis

updated at May 30, 2024, 2:10 p.m.

46 +0

621 +1

257 +0

CellProfiler by CellProfiler

An open-source application for biological image analysis

updated at May 30, 2024, 9:08 a.m.

44 +0

869 +3

366 +0

pycytominer by cytomining

Python package for processing image-based profiling data

updated at May 30, 2024, 7:23 a.m.

6 +0

68 +1

32 +0

imagepy by Image-Py

Image process framework based on plugin like imagej, it is esay to glue with scipy.ndimage, scikit-image, opencv, simpleitk, mayavi...and any libraries based on numpy

updated at May 30, 2024, 4 a.m.

81 +0

1,288 +1

329 +0

stardist by stardist

StarDist - Object Detection with Star-convex Shapes

updated at May 29, 2024, 4:28 p.m.

29 +0

828 +2

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cellfinder by brainglobe

Automated 3D cell detection in very large images

updated at May 29, 2024, 1:46 p.m.

15 +0

172 +2

39 +1

spotiflow by weigertlab

Accurate and efficient spot detection for microscopy data

updated at May 29, 2024, 1:36 p.m.

3 +0

43 +1

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