INDEPTH Imaris Training School

Monday, 04 January 2021


The INDEPTH Cost Action hosted a virtual IMARIS training school between December 7th-14th 2020. This was hosted by Celia Baroux at the University of Zürich in collaboration with Michael Mahlert from Bitplane AG who have developed the IMARIS software (

The event included 16 participants who each took part in training tutorials and then extensive hands-on activities. On day 1 the event kicked off with introductions where participants outlined their research topics and how they hoped that Imaris could improve their analysis.

Throughout Day 1 and Day 2 Michael Mahlert provided lectures on Imaris rendering, segmentation and Advanced features, which were interspersed with short practice sessions.

From Day 3 Celia Baroux provided working exercises for each participant that were linked to their own research projects, which they then worked on over the next three days. At the end of the training school they then presented what they had learnt and how they had used the Imaris software. All the while Celia was available to provide advice and throughout the event there appeared to be great interactions between participants to help each other with their exercises.

It was exciting to observe the progress that participants had made during the week to learn and explore the capabilities of the software. The reporting sessions were also useful as they demonstrated that some participants needed to improve the quality of their microscope images in order to gain maximum benefit from Imaris. 

An excellent example of a new usage of Imaris came from INDEPTH chair Christophe Tatout. Recently they had published a paper that looked at the chromatin organisation in an Arabidopsis kaku4crwn1crwn2 triple mutant, in which they had analysed images using NucleusJ (Dubos et al, 2020 Nucleus  doi: 10.1080/19491034.2020.1845012). Christophe had reanalysed their original data using Imaris and was able to accurately reproduce the localisation of both 180bp and 5S rRNA repeats. This confirmed that Imaris allows biologically relevant outputs as well as providing beautiful images.


Christophe Tatout presents Imaris rendering of a 2D image previously analysed by NucleusJ (doi: 10.1080/19491034.2020.1845012). The mutant is Arabidopsis kaku4crwn1crwn2.

Another convincing example comes from the analysis of SIM images by Ivona Kubalova and Veit Schubert (IPK Gatersleben) who experienced the power of in silico dissection for segmenting relevant part of the image, separating chromosome and FISH probe signals, for further volume, number and intensity measurements


Image processed after the data published in Marques et al (2016) doi: 10.1534/genetics.116.191213

As a final example, Isabelle Colas (James Hutton Institute, Dundee) designed an image processing pipeline to segment, count and measure colocalised signal in a supervised, semi-automated manner, from a complex semi-3D high-resolution (SIM) image of a meiotic tinsel structure at pachytene in barley. Video clip can be accessed here on Dropbox (


Gif generated from image processed after the data published in Colas et al (2017), Frontiers in Plant Science doi: 10.3389/fpls.2017.01235

To an outside observer of the training school it was clear that to gain maximum benefit from Imaris takes significant time in order to learn the intricacies of the software. Therefore a week-long immersive workshop is exactly what was needed to allow the participants to become sufficiently familiar with the software.

Enormous credit must go to Celia Baroux who after a challenging semester took an entire week to lead this training school. This was not a trivial undertaking and it is activities such as this that enable the INDEPTH Cost Action to be successful. Credit also to Michael Mahlert and Bitplane AG who provided their time and resources (in the form of virtual machines) for the training school.   

The next INDEPTH training school on analysis of Protein-Protein Interactions (PPI) will be held at the beginning of February, virtually hosted by Rafal Archaki and Marta Koblowska at the University of Warsaw. This event features both lectures and hands-on training opportunities so please encourage your lab-mates to consider signing up if interested.