Cell Invasion tool and nuclei counting

Added by Volker Baecker over 5 years ago

The tool allows to measure the area of the invading spheroïd in a 3D cell invasion assay. It can also count and measure the area of the nuclei within the spheroïd. Check out the tool on the wiki

BioImage Information Index (2 comments)

Added by Volker Baecker over 9 years ago

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:

MRI Artemia Tools online

Added by Volker Baecker almost 11 years ago

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.

enhancement of the root tools

Added by Volker Baecker almost 11 years ago

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

Ovocyte Tool

Added by Admin MRI almost 11 years ago

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.

Publication using the "Arabidopsis Seedlings Tool"

Added by Volker Baecker about 11 years ago

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.


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