ImageJ-macros: BioImage Information Index (2 comments)
The BioImage Information Index lists software packages, plate-forms, sample data and workflows for biological image analysis. It helps image analysts and biologists to find the right tools to solve a given image analysis problem. I participated in the taggathon that is part of the EuBIAS 2015. The aim of the taggathon was to kick-start the index by adding a large number of workflows. About 150 workflows have been added including a number of MRI's "Biological Image Analysis Toolsets".
You can access the BioImage Information Index here: biii.eu.
The MRI Artemia Tools are now available here.
The Artemia Tools help to calculate the normalized redness of Artemia in images. They have been used for
Rode NO, Lievens EJP, Flaven E, Segard A, Jabbour-Zahab R, Sanchez MI, et al.
Why join groups? Lessons from parasite-manipulated Artemia.
Ostfeld R, editor. Ecology Letters. 2013 Apr;16(4):493–501.
The new version provides a better way to measure the angle of the root by using two independent lines that intersect the base line.
It prevents the closing of the active window when pressing the m-button, if the active window is not the window of the zoomed region.
Find the new version at
The evaluation of the last ImageJ workshop by the participants is now online. You can find it under:
The tool acquires images from the live window of the camera and measures the surface of the ovocyte in the image in a configurable time interval.
See Ovocyte Tool for more information.
The new ImageJ workshop session will be from the 13.05 - 15.05. The new manuscript has been updated and converted to latex for a better layout. The next thing to do is now to update the exercises.
The Arabidopsis Seedlings Tool allows to measure the surface of green pixels per well in images containing multiple wells. It can be run in batch mode on a series of images. It writes a spreadsheet file with the measured area per well and saves a control image showing the green surface that has been detected per well.
This tool has been used for the system described in the publication:
Macherel D, Abdelilah BENAMAR, Pierart A, Baecker V, Avelange-Macherel M-H, Rolland A, Gaudichon S, Di Gioia L.
Simple system using natural mineral water for high-throughput phenotyping of Arabidopsis thaliana seedlings in liquid culture.
International Journal of High Throughput Screening 2013 Feb;1.
A new release is planned for the 11.10.2012. Currently the new version can be tested at
A description of how to use the new features can be found here:
The manuscript has been updated to correspond to the latest version of ImageJ. In the same time the form has been improved concerning the chapter headings and the illustrations.
The MRI Cell Image Analyzer (MRI-CIA) has been removed from the workshop. Due to improvements in ImageJ it is not needed for the workshop anymore.
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