Imaris – 3D image visualization and analysis course report

I attended a training session at the Bordeaux Faculty to learn how to use IMARIS, a software designed for viewing, measuring, and analyzing 3D microscopy images. The training, organized by the Bordeaux Imaging Center (BIC), was structured to first provide an overview of the software’s broad capabilities and then dig into more specific applications tailored to the participants’ research needs. The session, led by Sophie Allart and Sebastien Marais, both research engineers with expertise in imaging, lasted three days. During this time, we first revisited some basic imaging concepts before exploring participants’ individual research questions and how IMARIS could be used to extract precise and complex statistics from 3D images.

We began by learning how to reduce the size of an image to make it easier to handle. We then explored various techniques for cleaning up an image’s background, either by manually removing it or by creating a mask based on the desired fluorescent signal, effectively reducing noise outside the mask. One of the key features we examined was the spot creation tool, which is useful for counting and classifying cells. This tool assigns a point to each signal, providing spatial data such as distances between points and signal colocalization. Another valuable feature of IMARIS is the surface creation tool, which assigns volume to a signal, allowing measurements of whether objects are touching, overlapping, or how far apart they are, along with statistical analysis.

My primary goal was to gain expertise in analyzing neuronal dendritic spines morphology using the “Filament Tracer” tool. This tool is specifically designed for branched cells, like neurons and vasculature. It enables the detection and measurement of branching patterns (e.g., number, frequency, and degree), as well as the classification of dendritic spines into types (e.g., thin, stubby, mushroom, or filopodia).

Beyond providing detailed statistics for matrix and vector images, IMARIS also offers a 3D visualization of images, ideal for presentations or posters, and includes a movie-making feature that allows users to create short films from images, such as peeling through different layers of a biological sample.

Overall, this training provided me with a comprehensive understanding of IMARIS and its various strategies for answering specific scientific questions. It is now up to me to decide which approach and tools best suit my own research questions and samples.

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