ThermImageJ by gtatters

ImageJ functions and macros for working with thermal image files

created at April 19, 2019, 2:06 p.m.

8 +0

43 +0

6 +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

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

spotiflow by weigertlab

Accurate and efficient spot detection for microscopy data

created at Feb. 2, 2024, 5:28 p.m.

3 +0

45 +1

4 +0

minerva-story by labsyspharm

Minerva Story is an image viewer that is designed specifically to make it easy for non-expert users to interact with complex tissue images.

created at Dec. 16, 2019, 7:39 p.m.

12 +0

49 +0

14 +0

root_painter by Abe404

RootPainter: Deep Learning Segmentation of Biological Images with Corrective Annotation

created at April 16, 2020, 12:11 a.m.

5 +0

53 +0

11 +0

big-fish by fish-quant

Toolbox for the analysis of smFISH images.

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

8 +1

54 +0

18 +0

GPim by ziatdinovmax

Gaussian processes and Bayesian optimization for images and hyperspectral data

created at Feb. 18, 2020, 7:28 p.m.

6 +0

55 +0

7 +0

SMAP by jries

None

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

9 +0

61 +0

20 +0

nat by natverse

NeuroAnatomy Toolbox: An R package for the (3D) visualisation and analysis of biological image data, especially tracings of single neurons.

created at Jan. 2, 2014, 7:54 a.m.

17 +0

61 +0

26 +1

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

ark-analysis by angelolab

Integrated pipeline for multiplexed image analysis

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

10 +0

67 +0

24 +0

pyotf by david-hoffman

python functions for simulating optical transfer functions

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

7 +0

68 +1

15 +0

EBImage by aoles

Image processing toolbox for R

created at Aug. 15, 2014, 3:25 p.m.

13 +0

69 +1

28 +0

DeepMushroom by Olament

Image classification of Fungus using ResNet

created at Oct. 14, 2019, 4:50 a.m.

4 +0

69 +0

10 +0

pycytominer by cytomining

Python package for processing image-based profiling data

created at July 3, 2019, 6:22 p.m.

6 +0

70 +1

32 +0

wholebrain by tractatus

R package for segmentation, registration and generating web-based brain atlases from microscope images

created at Oct. 29, 2015, 5:43 p.m.

9 +0

80 +0

43 +0

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

DECODE by TuragaLab

This is the official implementation of our publication "Deep learning enables fast and dense single-molecule localization with high accuracy" (Nature Methods)

created at Aug. 6, 2020, 11:13 p.m.

7 +0

86 +1

26 +0

plant-seg by kreshuklab

A tool for cell instance aware segmentation in densely packed 3D volumetric images

created at Oct. 18, 2019, 10:56 a.m.

7 +0

86 +0

30 +0