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.

• Schedule

  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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