Program
Tuesday, May 13, 2025
08:30 – 10:30 | Installations Fiji, Anaconda, Python environments & packages. |
Coffee break | |
10:45 – 11:00 | Registration |
11:00 – 11:05 | Welcome | Martin Čapek (IMG) |
11:05 – 11:45 | Introduction into deep learning (DL) for image segmentation | Martin Čapek (IMG) |
11:45 – 12:15 | Image denoising (Noise2Void) | Jan Valečka (IMG) |
12:15 – 12:45 | Short introduction into Python | Martin Čapek (IMG) |
Lunch | |
13:30 – 14:50 | StarDist 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 – 16:05 | Cellpose 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 – 17:20 | Apeer.com: free available cloud platform for image processing including machine and deep learning. Lecture and Hands-On | Pavel Krist (Zeiss) Sponsor’s lecture. |
17:20 | End of the Day |
Wednesday, May 14, 2025
09:00 – 09:45 | Omnipose bacteria segmentation block | Michaela Blažíková (IMG) – Omnipose standalone app practicals using bacteria time-lapse data. – Python practicals (Jupyter notebook). |
09:45 – 11:00 | TrackMate block: tracking using DL segmentation models | Michaela Blažíková (IMG) – Short intro. – Fiji practicals using time-lapse images. |
Coffee break | |
11:15 – 13:00 | Google 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 – 15:45 | MitoSegNet 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 – 17:00 | Virtual Reality based image segmentation and measurement: a Toy Demo | Pavel Krist (Zeiss) Sponsor’s practicals. |
17:00 | Saying Good Bye |