cloud-volume by seung-lab

Read and write Neuroglancer datasets programmatically.

created at July 25, 2017, 5:34 p.m.

29 +0

126 +0

42 +0

RS-FISH by PreibischLab

Tool for precise, interactive, fast and scalable FISH spot detection

created at Oct. 4, 2017, 5:01 p.m.

12 +0

45 +0

13 +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

dypfish by cbib

Python library for statistical analysis of mRNA and protein distributions in fluorescent microscopy images

created at Dec. 15, 2017, 8:56 a.m.

7 +0

1 +0

1 +0

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

13 +0

2 +0

mia by mianalysis

Modular, object-based analysis for ImageJ/Fiji

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

2 +0

11 +0

2 +0

quanfima by rshkarin

Quanfima (Quantitative Analysis of Fibrous Materials)

created at April 2, 2018, 6:27 p.m.

2 +0

28 +0

16 +0

CaPTk by CBICA

Cancer Imaging Phenomics Toolkit (CaPTk) is a software platform to perform image analysis and predictive modeling tasks. Documentation: https://cbica.github.io/CaPTk

created at April 10, 2018, 1:36 p.m.

4 +0

172 +0

62 +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

CSBDeep by CSBDeep

Image restoration for fluorescence microscopy

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

21 +0

267 +1

82 +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.

14 +0

191 +2

68 -2

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

suite2p by MouseLand

cell detection in calcium imaging recordings

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

18 +0

329 +0

237 +1

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

OAD by zeiss-microscopy

Collection of tools and scripts useful to automate microscopy workflows in ZEN Blue using Python and Open Application Development tools and AI tools.

created at Oct. 27, 2018, 4:42 p.m.

18 +0

120 +0

47 +0

SMAP by jries

None

created at Nov. 2, 2018, 2:47 p.m.

9 +0

60 +0

19 -1

ddpsc_phenotypercv by jberry47

Header-only C++11 library using OpenCV for high-throughput image-based plant phenotyping

created at Nov. 7, 2018, 1:32 p.m.

2 +0

4 +0

0 +0

big-fish by fish-quant

Toolbox for the analysis of smFISH images.

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

7 +0

53 +0

18 +0

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

ark-analysis by angelolab

Integrated pipeline for multiplexed image analysis

created at Jan. 7, 2019, 4:31 a.m.

10 +0

66 +2

24 +0