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Fiji plugin for object(s) detection using template(s) matching
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Images Add wiki images Apr 26, 2019
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README.md

README.md

Introduction

Template matching is an algorithm that can be used for object-detections in images.
The algorithm computes the probability to find one (or several) template images provided by the user into a larger image.
For more theoretical details, see the section Template Matching : How does it work ?.

You can find a similar implementation in KNIME in this repo.

Citation

If you use this implementation for your research, please cite:

Multi-Template Matching: a versatile tool for object-localization in microscopy images;
Laurent SV Thomas, Jochen Gehrig
bioRxiv 619338; doi: https://doi.org/10.1101/619338

Related resources

This plugin is using OpenCV in Fiji thanks to IJ-OpenCV.

see also:
Domínguez, César, Jónathan Heras, and Vico Pascual. "IJ-OpenCV: Combining ImageJ and OpenCV for processing images in biomedicine." Computers in biology and medicine 84 (2017): 189-194.

Licence

Creative Commons License
The content of this wiki (including illustrations and videos) is licensed under a Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International License.

As a derived work of IJ-OpenCV, the source codes are licensed under GPL-3.

Origin of the work

This work has been part of the PhD project of Laurent Thomas under supervision of Dr. Jochen Gehrig at:

ACQUIFER a division of DITABIS AG
Digital Biomedical Imaging Systems AG
Freiburger Str. 3
75179 Pforzheim

Fish

Funding

This project has received funding from the European Union’s Horizon 2020 research and innovation program under the Marie Sklodowska-Curie grant agreement No 721537 ImageInLife.

ImageInLife MarieCurie

Examples

Zebrafish head detection

Fish

MontageHead

Dataset available on Zenodo
DOI

Medaka larvae detections

MedakaEgg

MontageEgg

Image courtesy Jakob Gierten (COS, Heidelberg)
Dataset available on Zenodo
DOI

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