Workshop on AI in microscopy

AI in microscopy

Background: Recent years have given us tremendous advances in methods using artificial intelligence to solve many different tasks: The deep learning model chatGPT [OpenAI 2021] demonstrates how we can interact with computers naturally, and the Segment Anything Model (SAM) [Kirillov March 2023] has shown that most segmentation tasks can be completed given enough examples.

Content: The participants will 1) get a quick overview of image processing methods and their names to provide a vocabulary for large language models; 2) get hands-on experience with free or cheap tools for image analysis. We will start with the well-known QuPath analysis program, then we will investigate Jupyter Notebooks and Python as general tools for image analysis, and finally, we will explore whether large-language models are a shortcut to image analysis in Python; and 3) we will discuss the advantages and caveats of the three approaches and discuss what can be done easily and when to contact a data scientist.

Target group: Microscope life scientists

Format: Alternating lectures and hands-on exercises. Bring your laptop. 

Participation fee includes: Lunch and refreshments.

Venue: The lectures will be held in Room 4A069 (building 4a, ground floor (0), room 69). The Islands Brygge Metro station is 2 minutes from the entrance and the room is right inside the building. The exercise rooms will be in the neighboring rooms.

Program: We have prepared an exciting programs for you with a mixture of lectures and try-it-yourself exercises. Lectures will be in a joint room, and for the exercises, you will be divided into 3 exercise classes.

Time	Activity	Responsible
09.30 - 10.00	Check-in, coffee and morning snacks
10.00 - 10.05	Welcome and introduction to workshop	Sporring, Jon; Hasselholt, Stine
10.05 - 10.50	QuPath: Image processing and object segmentation	Loo, Tricia Yi Jun
10.50 - 11.50	QuPath exercise: Measurements in 2D
11.50 - 12.50	Lunch
12:50 - 13:10	Lecture: The importance of the pipeline	Nørgaard, Martin
13.10 - 13.40	Python: Image processing and object segmentation	Sporring, Jon
13.40 - 14.55	Python exercise: Hands on python with starter script
14.55 - 15.15	Coffee break
15.15 - 15.45	Large language models: ChatGPT for image analysis	Haase, Robert
15.45 - 16.50	ChatGPT exercise: object segmentation and measurements
16.50 - 17.00	Summary and outlook	Hasselholt, Stine

Material: You will be working with 3 tools: QuPath, Python, and chatGPT. To avoid installation time, we ask that you pre-install QuPath and Anaconda (a Python interpreter and editing tools), and that you sign up for chatGPT.

Sponsor: We are happy to be sponsored in part by Danish Data Science Academy.

See also: The workshop is a part of the EMC2024 Conference.