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 June 6, 2024, 2:34 p.m.

47 +0

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LLSpy by tlambert03

Lattice light-sheet post-processing utility.

updated at June 6, 2024, 2:53 p.m.

8 +0

24 -1

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root_painter by Abe404

RootPainter: Deep Learning Segmentation of Biological Images with Corrective Annotation

updated at June 6, 2024, 3:11 p.m.

5 +0

53 +1

11 +0

brainglobe-atlasapi by brainglobe

A lightweight python module to interact with atlases for systems neuroscience

updated at June 6, 2024, 4:01 p.m.

10 +0

116 +2

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python-microscopy by python-microscopy

The python-microscopy environment - an open-source package for light microscopy

updated at June 6, 2024, 10:26 p.m.

9 +0

83 +0

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cloud-volume by seung-lab

Read and write Neuroglancer datasets programmatically.

updated at June 7, 2024, 12:45 a.m.

29 +0

126 +0

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paquo by Bayer-Group

PAthological QUpath Obsession - QuPath and Python conversations

updated at June 7, 2024, 3:48 a.m.

10 +0

100 +1

16 +0

ZeroCostDL4Mic by HenriquesLab

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

updated at June 7, 2024, 7:41 a.m.

35 -1

548 +2

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TrackMateR by quantixed

Analysis of TrackMate XML outputs in R

updated at June 7, 2024, 9:37 a.m.

3 +0

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cellpose by MouseLand

a generalist algorithm for cellular segmentation with human-in-the-loop capabilities

updated at June 7, 2024, 10:15 a.m.

30 +0

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cellfinder by brainglobe

Automated 3D cell detection in very large images

updated at June 7, 2024, 11:38 a.m.

15 +0

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axondeepseg by axondeepseg

Axon/Myelin segmentation using Deep Learning

updated at June 7, 2024, 2:49 p.m.

13 +0

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Cell_ACDC by SchmollerLab

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

updated at June 7, 2024, 2:50 p.m.

5 +0

120 +1

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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.

updated at June 7, 2024, 3:22 p.m.

17 +0

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brainrender by brainglobe

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

updated at June 7, 2024, 6:12 p.m.

18 +0

520 +3

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FAST-Pathology by AICAN-Research

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

updated at June 8, 2024, 12:27 a.m.

7 +0

117 +1

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fiji by fiji

A "batteries-included" distribution of ImageJ

updated at June 8, 2024, 8:35 a.m.

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napari by napari

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

updated at June 8, 2024, 9 a.m.

48 +0

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imagej2 by imagej

Open scientific N-dimensional image processing

updated at June 8, 2024, 9:22 a.m.

92 +0

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ImageJ by imagej

Public domain software for processing and analyzing scientific images

updated at June 8, 2024, 9:29 a.m.

48 +0

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