cellSAM by vanvalenlab

Codebase for "A Foundation Model for Cell Segmentation"

created at Feb. 14, 2024, 10:41 p.m.

4 +0

52 +1

8 +1

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

39 +1

7 +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

57 +0

7 +0

ZstackDepthColorCode by UU-cellbiology

Z-stack Depth Colorcode ImageJ FIJI plugin

created at Jan. 11, 2021, 3:31 p.m.

3 +0

21 +0

7 +0

spotiflow by weigertlab

Accurate and efficient spot detection for microscopy data

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

3 +0

57 +0

7 +0

HistoClean by HistoCleanQUB

HistoClean is a tool for the preprocessing and augmentation of images used in deep learning models. This easy to use application brings together the most popular image processing packages from across the python universe, meaning no more looking at documentation! HistoClean provides real time feedback to augmentations and preprocessing options. This allows users to evaluate their steps before implementation.

created at May 5, 2021, 3:38 p.m.

2 +0

27 +0

6 +0

cellshape by Sentinal4D

3D shape analysis using deep learning

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

2 +0

21 +0

6 +0

RhizoVisionExplorer by rootphenomicslab

Application to extract features from plant root images

created at Jan. 30, 2019, 4:59 p.m.

7 +0

14 +0

6 +0

brainreg-napari by brainglobe

Automated 3D brain registration in napari with support for multiple species and atlases.

created at July 2, 2021, 2:11 p.m.

5 +0

15 +0

6 +0

cellfinder-napari by brainglobe

Efficient cell detection in large images using cellfinder in napari

created at Jan. 22, 2021, 1:21 p.m.

4 +0

24 +0

6 +0

LLSpy by tlambert03

Lattice light-sheet post-processing utility.

created at July 4, 2017, 4:20 p.m.

8 +0

27 +0

6 +0

ThermImageJ by gtatters

ImageJ functions and macros for working with thermal image files

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

8 +0

45 +1

6 +0

XitoSBML by spatialsimulator

XitoSBML - the spatial SBML plugin for ImageJ

created at Nov. 3, 2016, 6:28 a.m.

5 +0

7 +0

5 +0

CellMigration by quantixed

Analysis of cell migration in Igor Pro

created at Aug. 19, 2015, 12:10 p.m.

5 +0

7 +0

5 +0

DetecDiv by gcharvin

DetecDiv provides a comprehensive set of tools to analyze time microscopy images using deep learning methods. The software structure is such that data can be processed either at the command line or using a graphical user-interface. Detecdiv classification models include : image classification and regression, semantic segmentation, LSTM networks to analyze data and image timeseries.

created at March 18, 2020, 1:57 p.m.

4 +0

8 +0

4 +0

BactMAP by vrrenske

gateway for segmentation data to Rstats & visualization with ggplot2 - in development

created at Oct. 4, 2016, 3:18 p.m.

1 +0

4 +0

4 +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

17 +0

4 +0

FFT by hsueh-lab

Fungal Feature Tracker (FFT): A tool to quantitatively characterize morphology and growth of filamentous fungi

created at May 14, 2019, 3:03 a.m.

2 +0

13 +0

3 +0

proseg by dcjones

Probabilistic cell segmentation for in situ spatial transcriptomics

created at June 29, 2023, 6:14 p.m.

5 +0

45 +1

2 +0

ijp-color by ij-plugins

Plugins for ImageJ - color space conversions and color calibration

created at April 28, 2014, 2:59 a.m.

5 +0

23 +0

2 +0