Python for BioImage Analysis
Python has quickly become the universal language for scientific computing and deep learning applications.
During this 2 day workshop, we will cover Python programming essentials and rapidly progress to practical bioimage analysis techniques through interactive, hands-on sessions. You will also learn how to utilize and programmatically access Napari, a powerful nD viewer; and deploy and train foundational bioimage analysis deep learning models such as U-NET and Cellpose.
The workshop includes dedicated time for participants to work with their own images, applying newly acquired skills under teachers supervision.
Scope: The workshop is directed to life scientists with relevant image analysis needs and bioimaging facility staff planning to support their users in image analysis.
Requirements: Participants are expected to bring a laptop, further instructions will be sent about one week before the workshop. No prior programming knowledge required!
Catering: Coffee breaks & lunch will be catered for both days.
Registration Fee: 300 DKK
Registration Deadline: 13th of January 2024
Programme
20th of January (Monday)
| 09:00 - 10:30 | Introduction to Basic Python Programming |
| 10:30 - 10:45 | Coffee break |
| 10:45 - 12:45 | Image Processing with Python |
| 12:45 - 13:45 | Lunch |
| 13:45 - 15:15 | Napari for BIA - Part I |
| 15:15 - 15:30 | Coffee break |
| 15:30 - 17:00 | Napari for BIA - Part II |
21st of January (Tuesday)
| 09:00 - 10:30 | Machine Learning for BioImage Analysis - Part I |
| 10:30 - 10:45 | Coffee break |
| 10:45 - 12:15 | Machine Learning for BioImage Analysis - Part II |
| 12:15 - 13:15 | Lunch |
| 13:15 - 14:30 | Machine Learning for BioImage Analysis - Part III |
| 14:30 - 15:15 | Image to Data |
| 15:15 - 15:30 | Wrap-Up & Coffee break |
| 15:30 - 17:00 | [Optional] Work on your own data |
Location
Lykeion, Room V11-604-1
Level 1, Building 28A
Syddansk Universitet (SDU), Odense
The location of the room can be navigated via the SDU indoor map.
About the Organisers
DBI Infra IACF
The Danish Bioimaging Infrastructure (DBI-Infra) Image Analysis Core Facility (IACF) provides open services in image analysis to life scientists and medical researchers. We offer both in-person and remote support, helping you to visualize, analyze, and extract quantitative information out of your bioimaging datasets from anywhere.
Our team of experts is here to discuss your image analysis needs, guide and train you in the most suitable software solutions, or develop a complete image analysis workflow tailored to your scientific project. We leverage an extensive hardware and software infrastructure designed for remote image analysis, including a pool of latest-generation workstations, innovative High Performance Computing and data exchange services, and a broad range of bioimage analysis software tools.
The facility actively promotes open science and the most efficient data sharing with the scientific community according to the FAIR principles. We are collaborating with the Danish e-Infrastructure Collaboration (DeiC), the Network of European BioImage Analysts (NEUBIAS) and Euro-BioImaging, and we are engaged in multiple training and dissemination activities.
Danish Molecular Biomedical Imaging Center (SDU)
DaMBIC's mission is to provide an open-access national bioimaging infrastructure. The facility provides cutting-edge bioimaging infrastructure and services at SDU, serving research groups across the faculties of Health Sciences (SUND), Engineering (TEK), and Natural Sciences (NAT). Additionally, DaMBIC extends its services to users from other Danish universities, as well as to international collaborators and companies.
Thanks to a dedicated bioimaging research environment, expert personal and national and international collaborations, DaMBIC offers the ideal environment for a national Bioimaging infrastructure which will support high level research as well as education and training. This has been recognized by DaMBIC becoming a node in Euro-BioImaging and a Nikon Center of Excellence, underscoring its expertise and the quality of the facility.
The Danish Molecular Biomedical Imaging Center (DaMBIC) operates under the leadership of Scientific Director Jonathan Brewer. It is further supported by the board of SDUimaging, which constitutes the steering committee. This structure supports a focused and strategic approach to advancing the center's objectives in molecular biomedical imaging at SDU.
DaMBIC is funded by infrastructure grants from the Danish Ministry of Science, which include collaborations with other national research infrastructures including DBN, CellX and NanoCHEM. DaMBIC is also funded by grants from the Novo Nordisk foundation and the Carlsberg foundation.
The daily operations of DaMBIC are administrated by Center Manager Morten Frendø Ebbesen, Imaging Specialist Anup Shrestha and Biomedical Laboratory Scientist Ulla Melchior Hansen.