python-microscopy by python-microscopy

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

created at Nov. 28, 2019, 2:12 a.m.

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cytominer-database by cytomining

A package for storing morphological profiling data.

created at Jan. 6, 2016, 9 p.m.

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flika by flika-org

An interactive image processing program for biologists written in Python.

created at May 27, 2015, 5:25 p.m.

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nd2reader by Open-Science-Tools

Pure Python library for reading NIS Elements ND2 images and metadata

created at Feb. 14, 2017, 3:47 p.m.

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thunderstorm by zitmen

ThunderSTORM: a comprehensive ImageJ plugin for SMLM data analysis and super-resolution imaging

created at May 3, 2015, 6:59 p.m.

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pytorch_connectomics by zudi-lin

PyTorch Connectomics: segmentation toolbox for EM connectomics

created at March 27, 2019, 4:13 p.m.

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MorphoLibJ by ijpb

Collection of mathematical morphology methods and plugins for ImageJ

created at Feb. 10, 2014, 1:49 p.m.

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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.

created at July 1, 2016, 6:49 a.m.

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YeaZ-GUI by rahi-lab

An interactive tool for segmenting yeast cells using deep learning.

created at March 29, 2020, 7:47 p.m.

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pathml by Dana-Farber-AIOS

Tools for computational pathology

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

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pyotf by david-hoffman

python functions for simulating optical transfer functions

created at Sept. 21, 2016, 3:02 p.m.

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squidpy by scverse

Spatial Single Cell Analysis in Python

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

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CompactionAnalyzer by davidbhr

Evaluates the fiber orientation and intensity around cells that compact collagen tissue as measure of contractile strength.

created at July 8, 2020, 11:32 a.m.

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aradeepopsis by Gregor-Mendel-Institute

A versatile, fully open-source pipeline to extract phenotypic measurements from plant images

created at Feb. 13, 2020, 3 p.m.

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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.

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mia by mianalysis

Modular, object-based analysis for ImageJ/Fiji

created at March 16, 2018, 11:43 a.m.

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paquo by Bayer-Group

PAthological QUpath Obsession - QuPath and Python conversations

created at July 6, 2020, 12:21 p.m.

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ASI_MTF by emx77

Imagej macro to calculate the MTF based on a knife edge measurement

created at March 15, 2018, 11:52 p.m.

2 +0

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pyImSegm by Borda

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

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

14 +0

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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.

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