My Job Shadowing visit to the Electron Microscopy Unit in Finland

Reflecting on a Week of Learning and Collaboration

My recent job shadowing experience in Finland at the University of Helsinki’s Electron Microscopy Unit made possible with support from the Euro-BioImaging EVOLVE project, was an inspiring and enriching journey, centered around mastering the latest tools for volume electron microscopy (vEM) data processing and visualization. Over the week, I had the privilege of being hosted by Eija Jokitalo and intensively learning from Ilya Belevich, an expert in the field who devoted his time to training me.

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Key Milestones Achieved

Throughout this immersive week, I deepened my understanding and practical expertise across several advanced applications:

• Advanced Alignment Tools for Complex vEM Datasets
  I focused on refining techniques for using alignment tools tailored for intricate datasets. These tools form the backbone of straightforward processing pipelines, which are essential for handling high-volume vEM data
• Implementation of AI-Powered Segmentation (SAM2 Module)
  We installed and tested the SAM2 module, a new AI-based tool available in the updated Microscopy Image Browser (MIB) for straightforward segmentation of 3D data stacks. This innovation promises to make segmentation tasks significantly faster and more accurate—a breakthrough I’m excited to bring back to my lab.
• Data Organization and Deep Learning (DL) Techniques for vEM
  A large part of my training was devoted to organizing data effectively for DL approaches. We worked on setting up the appropriate resolution and binning processes needed for prediction models, ensuring that the data quality aligns with DL requirements. This will be invaluable as I implement DL approaches in our own projects

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Strategy for Knowledge Dissemination

Our lab regularly holds workshops focused on vEM workflows, covering essential data processing and analysis techniques. I intend to integrate the newly acquired skills and tools into our course offerings. The first chance to share these updates will be in early December at a presentation in Brno, and I’m also thrilled to showcase these advancements at the Euro-BioImaging Virtual Pub, where I am scheduled to present. These insights will not only enhance the courses within our Czech Node but also benefit colleagues across Europe who collaborate with us.

Outreach and Collaboration Reflections

The time spent learning at the Finnish Advanced Microscopy Node was truly transformative. Ilya’s generosity with his time allowed us to deeply explore MIB’s new features, especially the SAM2 module. 

Together, we streamlined a simpler installation and integration process that will make MIB more accessible for others in our field.

Our training was hands-on, primarily conducted on my computer and Ilya’s, which allowed us to address real challenges directly, though it left us with fewer photo opportunities! I felt warmly welcomed throughout my visit, and I’m grateful for the professional support from the Helsinki team.

I’m already in touch with colleagues back home who use MIB, sharing insights and solutions tailored to their specific datasets. This visit has equipped me with tools and strategies that I’m ready to pass on, ensuring that others in our field can also benefit from these advanced techniques.

A Fulfilling Workshop Back in Prague

Just weeks after returning, I had the chance to conduct a hands-on workshop on MIB at BIOCEV in Prague hosted by Aleš Benda. This one-day session with five enthusiastic participants was my first solo teaching experience with the software, and it was incredibly rewarding!

Over seven hours, we explored:

• MIB’s Interface and Key Functions: From GUI basics to data loading, preprocessing, and segmentation, the workshop was packed with demonstrations and hands-on exercises.
• AI-Powered Tools and Deep Learning: Although we only touched on deep learning applications, participants were eager to learn more, sparking plans for a follow-up session to delve deeper into these advanced techniques.

The feedback was excellent, with participants asking insightful questions and actively engaging with the content. Their curiosity drove the workshop forward, inspiring me to develop a "cheat sheet" for new MIB users in Czech—a resource I hope will make the software more approachable for beginners.

I cannot express how much I enjoyed Euro-BioImaging’s Job Shadowing visit and how much it had given to me. The dissemination part was also a really pleasant experience, as it was completely new to me. We have already decided to do a second edition of the workshop sometime later. I’m excited to continue collaborating with the team in Helsinki, and I look forward to putting these new skills to use and sharing them with my colleagues across the Czech Republic and beyond.  - František K.