deepcell-tf by vanvalenlab

Deep Learning Library for Single Cell Analysis

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

17 +0

402 +1

90 -1

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.

9 +0

83 +0

25 +0

cytominer-database by cytomining

A package for storing morphological profiling data.

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

3 +0

10 +0

10 +0

flika by flika-org

An interactive image processing program for biologists written in Python.

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

7 +0

22 +0

1 +0

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.

5 +0

43 +0

28 +0

pytorch_connectomics by zudi-lin

PyTorch Connectomics: segmentation toolbox for EM connectomics

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

6 +0

168 +1

76 +2

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.

7 +0

65 +0

16 +0

YeaZ-GUI by rahi-lab

An interactive tool for segmenting yeast cells using deep learning.

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

1 +0

27 +0

14 +0

pathml by Dana-Farber-AIOS

Tools for computational pathology

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

12 +0

371 +1

81 +0

pyotf by david-hoffman

python functions for simulating optical transfer functions

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

7 +0

68 +0

14 -1

squidpy by scverse

Spatial Single Cell Analysis in Python

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

9 +0

401 +1

70 +0

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.

0 +0

7 +0

1 +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

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

80 -1

1,289 +0

329 +0

paquo by Bayer-Group

PAthological QUpath Obsession - QuPath and Python conversations

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

10 +0

100 +0

16 +0

pyImSegm by Borda

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

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

14 +0

370 +2

73 +0

cellshape by Sentinal4D

3D shape analysis using deep learning

created at June 21, 2022, 11:25 a.m.

2 +0

20 +0

6 +0

neurite by adalca

Neural networks toolbox focused on medical image analysis

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

21 +0

325 +1

65 +0

Cell_ACDC by SchmollerLab

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

created at Feb. 25, 2021, 4:14 p.m.

5 +0

121 +1

20 +0

big-fish by fish-quant

Toolbox for the analysis of smFISH images.

created at Dec. 17, 2018, 12:26 p.m.

8 +0

54 +0

18 +0

ZetaStitcher by lens-biophotonics

ZetaStitcher is a tool designed to stitch large volumetric images such as those produced by Light-Sheet Fluorescence Microscopes.

created at Nov. 7, 2017, 10:11 a.m.

6 +0

37 +0

6 +0