Deep Learning for Image Analysis

20 Oct 2025, 09:00 → 24 Oct 2025, 18:00 Europe/Berlin

European Neuroscience Institute Göttingen

Constantin Pape (UMIN), Antonio Politi (Facility for Light Microscopy, MPI-NAT, Göttingen), Martin Schilling (UKEI), Luca Freckmann (UMIN)

Additional tools

entrance_eni.jpg

Github link to course material

HCS-DL-Course-25_before_the_course.pdf

Map to ENI

lecture_slides

• 1_intro_to_dl.pdf
• 2_transfer_learning_and_sementation.pdf
• 3_deep_learning_tools.pdf
• 4_conclusion.pdf

Monday 20 October

09:00 → 12:30 Classification

09:00 Lecture: Intro to DL for microscopy, classification and PyTorch

10:30 Getting started

• Participant introductions
• Setting up JupyterHub server
• Introducing first exercise on classification

12:30 → 13:30 Lunch

13:30 → 17:00 Classification

13:30 First exercise: Cell classification

16:30 Recap first exercise

Tuesday 21 October

09:00 → 12:30 Segmentation

09:00 Lecture: Segmentation, pre-trained models, transfer learning

10:30 Intro to exercises for Nucleus and Cell segmentation

12:30 → 13:30 Lunch

13:30 → 17:00 Segmentation

13:30 Second exercise: Cell segmentation

16:00 Recap exercise 2. Image restoration and lecture recap.

Wednesday 22 October

09:00 → 12:30 Other deep learning tools

09:00 Lecture: Overview of deep learning tools (micro-sam, cellpose, stardist, nn UNet, trackstra, ...)

10:30 Intro to third exercise

12:30 → 13:30 Lunch

13:30 → 17:45 Other deep learning tools

13:30 Third exercise: Group work where we try a tool per group

16:00 Recap third exercise, project discussion

Thursday 23 October

09:00 → 12:30 Project work

12:30 → 13:30 Lunch

13:30 → 17:00 Project work

Friday 24 October

09:00 → 12:30 Project work

12:30 → 13:30 Lunch

13:30 → 15:00 Project work

15:00 → 17:00 Final discussion

Wrap-up and how to continue to use the infrastructure