atomai by pycroscopy

Deep and Machine Learning for Microscopy

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

11 +0

191 +0

40 +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.

13 +0

193 +0

68 +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

201 +0

51 +0

CSBDeep by CSBDeep

Image restoration for fluorescence microscopy

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

21 +0

281 +2

82 +0

micro-sam by computational-cell-analytics

Segment Anything for Microscopy

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

7 +0

332 +5

41 +1

neurite by adalca

Neural networks toolbox focused on medical image analysis

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

21 +0

333 +2

67 +0

ilastik by ilastik

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

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

40 +0

348 +1

129 -1

suite2p by MouseLand

cell detection in calcium imaging recordings

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

18 +0

348 +3

240 +1

pyImSegm by Borda

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

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

14 +0

373 +0

73 +0

pathml by Dana-Farber-AIOS

Tools for computational pathology

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

13 +0

387 +0

82 +1

n2v by juglab

This is the implementation of Noise2Void training.

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

19 +0

392 +0

107 +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

394 +0

85 +0

deepcell-tf by vanvalenlab

Deep Learning Library for Single Cell Analysis

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

16 -1

412 +0

95 +1

squidpy by scverse

Spatial Single Cell Analysis in Python

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

9 +0

425 +1

78 +2

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

484 +0

137 +0

SimpleElastix by SuperElastix

Multi-lingual medical image registration library

created at Nov. 20, 2014, 9:51 a.m.

22 +0

509 +0

149 +0

brainrender by brainglobe

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

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

17 +0

540 +2

76 +1

ImageJ by imagej

Public domain software for processing and analyzing scientific images

created at Aug. 1, 2011, 12:29 p.m.

50 +0

551 +3

221 +0

ZeroCostDL4Mic by HenriquesLab

ZeroCostDL4Mic: A Google Colab based no-cost toolbox to explore Deep-Learning in Microscopy

created at Feb. 12, 2020, 9:18 a.m.

35 +0

555 +2

129 +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.

46 +0

626 +2

365 +1