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3D Spatial Analysis Using Mica's AI-Enabled Microscopy Software

Extracting publication-grade insights from 3D Paramecium tetraurelia data

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Protist Paramecium (Paramecium tetraurelia) stained to show the nucleus Protist_Paramecium__Paramecium_tetraurelia__stained_to_show_the_nucleus.jpg

This video offers practical advice on the extraction of publication grade insights from microscopy images. Our special guest Luciano Lucas (Leica Microsystems) will illustrate how Mica’s AI-enabled software can be used to start the 3D spatial image analysis process. He will then deep dive into two Mica 3D images and explore spatial relationships between the different visible biological elements. The session concludes with the creation of high-fidelity video animations and other publication ready outputs. 

To watch the full experiment, simply fill in a few details in the form below to get your video on demand.

Key Learnings:

  • How to perform an initial rapid quantitative review of a 3D dataset of a paramecium
  • How to explore relationships between biological elements (e.g. organelles, cells, tissue regions) and organisms
  • How to perform a spatial analysis of a paramecium dataset
  • Learn how to easily create high impact SciCom materials such as video animations, charts and stills
Paramecicum rendering with AIVIA
Figure 1: Creating high impact sci-com materials. Image shows Paramecium tetraurelia rendered with Aivia. Nucleus, organism, basal bodies and cilia color coded by distance to the nucleus.

The Experiment

In this video, our expert image analyst Luciano Lucas illustrates how to use Mica’s AI-enabled software to start the 3D image analysis process. Using a 3D dataset of the unicellular organism Paremecium tetaurella, we learn how to segment 4 different structures including the cilia, nucleus and basal bodies.  We then explore the spatial relationships between the different visible biological elements and learn how to create graphs and charts quantifying these relationships. Luciano demonstrates different options for presenting data including colour coding that allows you to best communicate your findings to your audience. The session concludes with the creation of high-fidelity video animations and other publication ready outputs.

Protist Paramecium (Paramecium tetraurelia) stained to show the nucleus, basal body, a protein ring, the epiplasm, a thin dense layer at the base of a cilia where basal bodies are inserted and the cilia.
Figure 2: Image shows a protist Paramecium (Paramecium tetraurelia) stained to show the nucleus (Hoechst, white), the basal body, a protein ring found at the base of a cilium (AF488, green), the epiplasm, a thin dense layer at the base of a cilia where basal bodies are inserted (AF568, red) and the cilia (Star635P, blue). Images were acquired on Mica with HC PL APO CS2 63x/1.20 water objective using Lightning grade and processing with +5 sample protection. Sample courtesy: A. Aubusson-Fleury, CNRS, GIF sur Yvette, France.

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