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ImageJ Macro Tool Sets for Biological Image Analysis

Abstract

At the imaging facility Montpellier RIO Imaging we create custom solutions for image analysis and automation tasks based on ImageJ. We provide these solutions in the form of ImageJ macro tool sets. Macro tool sets are easy to install, provide a simple graphical interface, allow to set options and can call plugins for more complex tasks. The first button of each tool set opens the help and installation page of the tool set on the wiki of the facility's project management and task-tracking tool. The wiki contains installation and usage instructions, the tool set macro, links to plugins and other dependencies and example images. A tool set often contains a manual version of the macro that can be used to test the macro on the current image and a batch version that will run the same macro on a set of images.

The general approach and a number of available tool sets will be presented here. The tool sets for biological image analysis include: the segmentation of adipocytes, the analysis of multi-well arabidopsis seedling images, the counting of segment like objects, the analysis of virus infections in leaves, the measurement of the interdigitation index and the thickness in skin images and the analysis of wound healing. The tool sets concerning the workflow include: the cropping of regions from big images, the conversion of image formats, the navigation within a set of images, the transformation of ROIs and the order of ROIs in the ROI-manager.

Keywords

ImageJ, microscopy, image analysis, macros, tool sets, automation

Short CV

Volker Bäcker studied computer science and physics at the University of Dortmund. He worked as a software developer and consultant for the company Georg Heeg eK, specialized in object oriented analysis and design and implementations in Smalltalk. Since 2004 he works for the imaging facility Montpellier RIO Imaging. Part of his work at MRI is the development of image analysis tools based on ImageJ.

Administrative data

Presenting author: Volker Baecker
Organisation: Montpellier RIO Imaging

co-authors:

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