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

empanada by volume-em

Panoptic segmentation algorithms for 2D and 3D electron microscopy images

created at Dec. 1, 2021, 4:02 p.m.

1 +0

1 +0

0 +0

ZFVascularQuantification by ElisabethKugler

#ZVQ - Zebrafish Vascular Quantification - https://doi.org/10.1242/dev.199720

created at Aug. 10, 2020, 1:59 p.m.

2 +0

10 +0

0 +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

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

TrackMateR by quantixed

Analysis of TrackMate XML outputs in R

created at Jan. 30, 2022, 3:42 p.m.

3 +0

10 +0

1 +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

em-scalebartools by lukmuk

Fiji/ImageJ macros to quickly add a scale bar to an (electron microscopy) image.

created at Aug. 10, 2021, 9:41 a.m.

2 +0

11 +0

1 +0

htsimaging by rraadd88

🔬Python package for high-throughput single-cell imaging analysis.

created at Feb. 21, 2016, 10:25 a.m.

2 +0

5 +0

1 +0

QuimP by CellDynamics

QuimP is software for tracking cellular shape changes and dynamic distributions of fluorescent reporters at the cell membrane.

created at Jan. 24, 2017, 11:12 a.m.

5 +0

6 +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

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

22 +0

2 +0

cellSAM by vanvalenlab

Codebase for "A Foundation Model for Cell Segmentation"

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

4 +0

9 +0

3 +1

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 +1

3 +0

spotiflow by weigertlab

Accurate and efficient spot detection for microscopy data

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

3 +0

39 +0

3 +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

3 +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

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

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