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AI-Enabled Spatial Analysis of Complex 3D Datasets

How to extract publication grade insights from microscopy images - MicaCam Episode 05 - Video On Demand

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

This edition of MicaCam 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 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 MicaCam experiment, simply fill in a few details in the form below to get your video on demand, and access even more exclusive experiments in the MicaCam library.

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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

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Speakers

Dr. Luciano Lucas , Director Data & Analysis – Leica Microsystems

Luciano received his PhD in Tumour Angiogenesis and Vascular Targeting Drugs from the University of Nottingham, United Kingdom. In the last 15 years Luciano has been focused on extracting spatial insights from nD microscopy images. He was heavily involved in the development of Imaris (Oxford Instruments / Andor / Bitplane) and lead the creation of Aivia (SVision / DRVision). Luciano joined Leica Microsystems in 2021 when it acquired SVision. He is now the Director for Data & Analysis for Leica Microsystems and is focused on Aivia / AiviaWeb and a range of data, image analysis and AI projects which will result in smarter Leica imaging systems in the future.

Dr. Lynne Turnbull

Dr. Lynne Turnbull, Senior Application Manager – Leica Microsystems

Lynne is a Senior Application Manager at Leica Microsystems. She received her PhD in Sydney Australia in cardiac biophysics and undertook postdoctoral training in San Francisco and Melbourne. Upon moving to the University of Technology Sydney, Lynne established and managed the Microbial Imaging Facility. Lynne joined Leica Microsystems in 2021 as a Senior Application Manager and is based at the EMBL IC in Heidelberg.

The Experiment

MicaCam Episode 05 - original broadcast date: 15th June 2022

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 1: 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.

In this episode, our expert image analyst Luciano Lucas illustrates how to use Mica’s AI-enabled software to start the 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.

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Paramecicum rendering with AIVIA
Figure 2: 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.

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