Program
Monday 18 May 2026
| Meeting room 0.117 | |
|---|---|
| 14:00 – 16:00 | Installations (voluntary if any problem arises) |
Tuesday 19 May 2026
| Lecture room 0.195 | |
|---|---|
| 09:00 – 09:30 | Registration + Fast Installation Checking + Coffee |
| 09:30 – 09:35 | Welcome |
| 09:35 – 09:50 | Course overview – methods vs. applications | Martin Čapek (IMG) |
| 09:50 – 10:10 | Anaconda + Python overview | Jan Valečka (IMG) |
| 10:10 – 10:55 | Introduction into deep learning (DL) for image segmentation | Martin Čapek (IMG) |
| Coffee break | |
| 11:10 – 11:40 | Image denoising (Noise2Void) | Jan Valečka (IMG) |
| 11:40 – 12:20 | Short introduction into Python | Martin Čapek (IMG) |
| Lunch | |
| 13:20 – 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 – 17:05 | arivis.cloud: free available cloud platform for image processing including machine and deep learning. Lecture and demo | Pavel Krist (Zeiss) Sponsor’s lecture. |
| 17:05 | End of the Day |
Wednesday 20 May 2026
| Lecture room 0.195 | |
|---|---|
| 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 – 10:45 | TrackMate block: tracking using DL segmentation models | Michaela Blažíková (IMG) – Short intro. – Fiji practicals using time-lapse images. |
| Coffee break | |
| 11:00 – 13:00 | 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. |
| Lunch | |
| 14:00 – 14:30 | DeepImageJ – various applications of DL methods to image processing | Michaela Blažíková (IMG) |
| 14:30 – 16:00 | 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. |
| Coffee break | |
| 16:15 – 16:45 | Virtual Reality based image segmentation and measurement: a Toy Demo | Pavel Krist (Zeiss) Sponsor’s practicals. |
| 16:45 | End of the Day |
Thursday 21 May 2026
| Lecture room 0.195 | |
|---|---|
| 09:00 – 11:00 | Independent solving of practical tasks based on the lessons taught + discussions, Part 1 |
| Coffee break | |
| 11:15 – 13:15 | Independent solving of practical tasks based on the lessons taught + discussions, Part 2 |
| 13:15 – 13:30 | Course evaluation |
| 13:30 | End of the Course |