Program

Tuesday, May 13, 2025

08:30 – 10:30Installations
Fiji, Anaconda, Python environments & packages.
Coffee break
10:45 – 11:00Registration
11:00 – 11:05Welcome | Martin Čapek (IMG)
11:05 – 11:45Introduction into deep learning (DL) for image segmentation | Martin Čapek (IMG)
11:45 – 12:15Image denoising (Noise2Void)  | Jan Valečka (IMG)
12:15 – 12:45Short introduction into Python | Martin Čapek (IMG)
Lunch
13:30 – 14:50StarDist segmentation block | Martin Čapek (IMG)
– Fiji practicals using 2D/3D images of various images and quality.
– Python practicals (Jupyter notebook) using a large image.
14:50 – 16:05Cellpose segmentation block    | Jan Valečka (IMG)
– Fiji practicals using 2D/3D images, macro example.
– Cellpose standalone app practicals, retraining the model for new images.
Coffee break
16:20 – 17:20Apeer.com: free available cloud platform for image processing including machine and deep learning. Lecture and Hands-On | Pavel Krist (Zeiss)
Sponsor’s lecture.
17:20End of the Day

Wednesday, May 14, 2025

09:00 – 09:45Omnipose bacteria segmentation block | Michaela Blažíková (IMG)
– Omnipose standalone app practicals using bacteria time-lapse data.
– Python practicals (Jupyter notebook).
09:45 – 11:00TrackMate block: tracking using DL segmentation models | Michaela Blažíková (IMG)
– Short intro.
– Fiji practicals using time-lapse images.
Coffee break
11:15 – 13:00Google Colab block: cloud-based distant computing | Michaela Blažíková (IMG)
– Delta2 – bacteria tracking package using DL segmentation/tracking models.
– ZeroCostDL4Mic practicals demos to process microscopy data.
Lunch
13:45 – 15:45MitoSegNet block: mitochondrial segmentation and morphology analysis | Martin Čapek (IMG)
Demo of the full process of DL-based analysis including image annotations, model retraining and morphological analysis.

– MitoSegNet standalone app – mitochondrial segmentation.
– Labkit plugin in Fiji – annotations of new mitochondrial images.
– MitoSegNet standalone app – retraining the model by using the annotated images.
– MitoSegNet standalone app – statistical morphological analysis of new segmented images.
Coffee break
16:00 – 17:00Virtual Reality based image segmentation and measurement: a Toy Demo | Pavel Krist (Zeiss)
Sponsor’s practicals.
17:00Saying Good Bye