RhizoVisionExplorer by rootphenomicslab

Application to extract features from plant root images

updated at Sept. 12, 2024, 9:22 a.m.

7 +0

13 +0

7 +0

stardist by stardist

StarDist - Object Detection with Star-convex Shapes

updated at Sept. 12, 2024, 3:42 p.m.

26 +0

895 +0

218 +1

cytominer-database by cytomining

[DEPRECATED] A package for storing morphological profiling data.

updated at Sept. 13, 2024, 4:36 p.m.

3 +0

10 +0

10 +0

pytorch_connectomics by zudi-lin

PyTorch Connectomics: segmentation toolbox for EM connectomics

updated at Sept. 13, 2024, 9:57 p.m.

6 +0

171 +0

77 +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

updated at Sept. 14, 2024, 1:51 a.m.

80 +0

1,302 +0

333 +1

deepcell-tf by vanvalenlab

Deep Learning Library for Single Cell Analysis

updated at Sept. 14, 2024, 5:36 p.m.

16 -1

412 +0

95 +1

thunderstorm by zitmen

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

updated at Sept. 15, 2024, 9:12 a.m.

19 +0

93 +0

42 +0

TrackMate by trackmate-sc

TrackMate is your buddy for your everyday tracking.

updated at Sept. 15, 2024, 10:34 a.m.

20 +0

160 +0

75 +0

SMAP by jries

None

updated at Sept. 15, 2024, 12:36 p.m.

9 +0

63 +0

20 +0

pycytominer by cytomining

Python package for processing image-based profiling data

updated at Sept. 16, 2024, 8:49 p.m.

6 +0

76 +0

34 +0

ark-analysis by angelolab

Integrated pipeline for multiplexed image analysis

updated at Sept. 17, 2024, 12:39 p.m.

10 +0

72 +1

25 +0

CSBDeep by CSBDeep

Image restoration for fluorescence microscopy

updated at Sept. 18, 2024, 7:51 a.m.

21 +0

281 +2

82 +0

MorphoLibJ by ijpb

Collection of mathematical morphology methods and plugins for ImageJ

updated at Sept. 18, 2024, 11:40 a.m.

17 +0

101 +1

48 +0

CellProfiler by CellProfiler

An open-source application for biological image analysis

updated at Sept. 18, 2024, 5:55 p.m.

45 +0

893 +0

377 +2

cellSAM by vanvalenlab

Codebase for "A Foundation Model for Cell Segmentation"

updated at Sept. 19, 2024, 2:58 a.m.

4 +0

37 +1

7 +0

ilastik by ilastik

ilastik-shell, applets, and workflows to string them together.

updated at Sept. 19, 2024, 3:51 a.m.

40 +0

348 +1

129 -1

python-microscopy by python-microscopy

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

updated at Sept. 19, 2024, 6:41 a.m.

9 +0

83 +0

25 +0

Cell_ACDC by SchmollerLab

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

updated at Sept. 19, 2024, 9:04 a.m.

4 +0

127 +1

21 +0

plantcv by danforthcenter

Plant phenotyping with image analysis

updated at Sept. 19, 2024, 9:42 a.m.

45 -1

646 +2

263 +0

picasso by jungmannlab

A collection of tools for painting super-resolution images

updated at Sept. 19, 2024, 2:05 p.m.

15 +0

109 +0

50 +1