Deep Learning for Image Analysis

Oct 20, 2025, 9:00 AM → Oct 24, 2025, 6:00 PM 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

Mon, October 20

9:00 AM → 12:30 PM Classification

9:00 AM Lecture: Intro to DL for microscopy, classification and PyTorch

10:30 AM Getting started

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

12:30 PM → 1:30 PM Lunch

1:30 PM → 5:00 PM Classification

1:30 PM First exercise: Cell classification

4:30 PM Recap first exercise

Tue, October 21

9:00 AM → 12:30 PM Segmentation

9:00 AM Lecture: Segmentation, pre-trained models, transfer learning

10:30 AM Intro to exercises for Nucleus and Cell segmentation

12:30 PM → 1:30 PM Lunch

1:30 PM → 5:00 PM Segmentation

1:30 PM Second exercise: Cell segmentation

4:00 PM Recap exercise 2. Image restoration and lecture recap.

Wed, October 22

9:00 AM → 12:30 PM Other deep learning tools

9:00 AM Lecture: Overview of deep learning tools (micro-sam, cellpose, stardist, nn UNet, trackstra, ...)

10:30 AM Intro to third exercise

12:30 PM → 1:30 PM Lunch

1:30 PM → 5:45 PM Other deep learning tools

1:30 PM Third exercise: Group work where we try a tool per group

4:00 PM Recap third exercise, project discussion

Thu, October 23

9:00 AM → 12:30 PM Project work

12:30 PM → 1:30 PM Lunch

1:30 PM → 5:00 PM Project work

Fri, October 24

9:00 AM → 12:30 PM Project work

12:30 PM → 1:30 PM Lunch

1:30 PM → 3:00 PM Project work

3:00 PM → 5:00 PM Final discussion

Wrap-up and how to continue to use the infrastructure