scikit-image by scikit-image

Image processing in Python

created at July 7, 2011, 10:07 p.m.

186 +0

5,907 +6

2,207 +2

napari by napari

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

created at Aug. 13, 2018, 1:12 a.m.

48 +0

2,086 +9

411 +2

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

created at Dec. 29, 2016, 7:35 a.m.

81 +0

1,288 +1

329 +0

CellProfiler by CellProfiler

An open-source application for biological image analysis

created at April 5, 2011, 12:10 p.m.

44 +0

869 +3

366 +0

stardist by stardist

StarDist - Object Detection with Star-convex Shapes

created at June 26, 2018, 7:54 p.m.

29 +0

828 +2

213 +0

plantcv by danforthcenter

Plant phenotyping with image analysis

created at March 14, 2014, 6:24 p.m.

46 +0

621 +1

257 +0

CaImAn by flatironinstitute

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

created at Aug. 6, 2015, 1:58 p.m.

47 +0

610 +1

356 +0

brainrender by brainglobe

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

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

18 +0

517 +4

75 +1

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

135 +0

squidpy by scverse

Spatial Single Cell Analysis in Python

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

9 +0

399 +4

71 +0

deepcell-tf by vanvalenlab

Deep Learning Library for Single Cell Analysis

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

16 +0

393 +1

91 +0

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.

10 +0

382 +0

84 +2

n2v by juglab

This is the implementation of Noise2Void training.

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

19 +0

378 +2

107 +1

pathml by Dana-Farber-AIOS

Tools for computational pathology

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

12 +0

368 +1

81 +2

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

ilastik by ilastik

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

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

41 +0

338 +0

130 +0

neurite by adalca

Neural networks toolbox focused on medical image analysis

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

21 +0

320 +1

65 +0

CSBDeep by CSBDeep

Image restoration for fluorescence microscopy

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

21 +0

267 +1

82 +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

195 +0

50 +0

atomai by pycroscopy

Deep and Machine Learning for Microscopy

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

11 +0

182 +1

38 +0