Welcome to two days of hands-on imaging and hackathon on tomography!
Title: Hands-on workshop and hackathon on tomography
When: 11–12 October, 9:00–16:00
Where: Workshop room on the 5th floor of LINXS (Scheelevägen 19), and the 4D imaging Lab at Lund University, Lund, Sweden
Target audience: Scientists working with x-ray or neutron imaging who would like to learn more about tomography and 3D image analysis and/or would like help with image analysis challenges to extract details from their 3D data. This workshop and hackathon is in the context of the Northern Lights on Food Theme at LINXS and so there is a focus towards food science related applications, but we welcome researchers from other fields also.
Pre-requisites: Both researchers that have never done a tomography experiment before, and those who have some preliminary data are invited.
For those that have their own data collected, to help us prepare, please provide a short description of the data and the scientific questions that you are trying to answer with the data (what would you like to extract from the images).
Please note that the event is limited to 25 participants, and the registration will close when full!
You might also be interested in the NLF tomography workshop 9–10 October: Link to event
Description:
Scientists interested in performing tomography or have already acquired their first data, will meet and work with experts in image visualisation, image analysis, to work together to visualise, quantify and interpret the scientific content in their 3D images. The event will start with an experiment at the 4D lab at Lund University, followed by talks and tutorials on image reconstruction, image segmentation, and introduction to different softwares that can be used for analysis of tomography data. The afternoon of the last day, will be focused on people who have their own data so that they discuss with image analysis experts their queries so that different solutions and analysis approaches can be determined. In addition, establishing continuing collaborations is a usual outcome after 2 days of sitting working closely together.
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11 October
09:00–11:30 Visit and “hands-on” imaging at the 4D imaging lab - including interactive discussions about imaging parameters, potential artefacts and mitigation, reconstruction, etc.
12:00–13:00 Lunch at LINXS
13:00–15:00 Introductory lectures:
Lecture 1: Tomography acquisition through reconstruction to images: theory, algorithms, practical aspects, what to think about, artifacts, absorption vs phase contrast etc.
Lecture 2: Introduction to image analysis and image segmentation
15:00–15:30 Coffee break
15:30–17:00 Introduction to image handling and treatment with Python
12 October
09:00–09:45 Introduction to Dragonfly software (online presentation by ORS)
09:45–10:00 Coffee break
10:00–12:00 Hands-on image analysis
• Introduction to 3D/4D image treatment and visualisation in ImageJ/Fiji
• Image handling plus semantic and instance segmentation example in Matlab® (cellulose foam example to segment, label and measure bubble sizes)
12:00–13:00 Lunch
13:00–16:00 Interactive discussions around participants’ data challenges (coffee break at 15:00)
Organisers:
For specific questions to the organisers, please contact
Niklas Lorén – niklas.loren@ri.se or
Stephen Hall - stephen.hall@solid.lth.se
For practical questions about the workshop, please contact josefin.martell@linxs.lu.se
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