Morphology Workshop 2023 “Approaches, Ideas and Solutions in Imaging”
Organizer: Thomas Schwaha (University of Vienna), Stephan Handschuh (Veterinary University of Vienna), Andy Sombke (Medical University of Vienna)
Morphological imaging techniques and analysis pipelines are constantly evolving. Rapid technological advancements make it highly challenging to keep up-to-date even for established researchers, while for young scientist the number of available imaging solutions is often overwhelming. Five questions are central when planning imaging-based morphological studies: (1) Which is the best imaging technique for my research question? (2) Do I need a single technique or a combination of two or more modalities in a correlative imaging approach? (3) How can I access the required imaging infrastructure as well as hard- and software for data visualization and analysis? (4) How can I receive adequate training to properly handle complex imaging systems? (5) How can I receive funding for imaging experiments?
The workshop aims at sharing expertise on microscopic imaging modalities, correlative imaging pipelines, as well as image visualization and analysis with early career scientists. In addition, Baubak Bajoghli (Managing Director of Austrian BioImaging) will give valuable insights on how to access imaging infrastructures that are not directly available to scientists at their own research institute. Hence, we consider this workshop as an opportunity to acquire skills for planning and conducting imaging-based morphological investigations.
The first part will be an online meeting taking place on March 31st. Registered attendants will present their projects in a 10-minute presentation, focusing on research questions, including taxa and structures of interest, used imaging technique(s) and potentially used correlative workflows, potential problems in sample preparation and imaging procedure, and/or potential problems in data visualization and analysis. After the presentations, organizers and workshop participants will provide feedback and share expertise to solve presented problems. Some of the discussed topics and tasks will be selected for the second part of the workshop, which will take place as a three-day on-site workshop (24.-26.05.2023) in Vienna. There, we will offer lectures on the theoretical background of imaging methods as well as correlative approaches and software solutions. Hands-on computer sessions will cover selected topics from participant projects including image processing (e.g., noise removal, re-orientation of datasets, reducing data size without losing quality), image registration and fusion, image segmentation and visualization (volume rendering, surface models), and others. Furthermore, hands-on sessions on microscopes will focus on the choice of the most suitable and cost-efficient imaging equipment, by comparing expensive high-end systems with new desktop imaging solutions. Our aim is to receive several desktop systems such as electron, fluorescence and confocal microscopes and together with application specialists analyze samples from workshop participants. Participants are encouraged to bring data acquired at their home institutions using high-end systems, and compare their data with on-site generated data from small desktop systems acquired during the demo sessions.
Since the number of participants is limited to 15, a max. one-page motivation letter should be sent to firstname.lastname@example.org until February 28th 2023.
online meeting with short presentations and group discussion
9. and 11. 05.
online introduction to Leica Mica, Phenom SEM and Schaefer-tec Tomocube
Demo for guests
18:00 Icebreaker – D’Landsknecht
09:00 Introduction to Light Microscopy with practical session
11:30 Introduction to Electron Microscopy
12:30 Lunch break
13:30 – 15:15 Practical Session 1 – Instrument Demo (Mica, SEM, Tomocube) and Computer Session
15:15 – 17:00 Practical Session 2 – Instrument Demo (Mica, SEM, Tomocube) and Computer Session
09:00 Introduction to MicroCT with practical session, Staining, Multiscale tomography, Dual energy
12:30 Lunch break
13:30 – 15:15 Practical Session 3 – Instrument Demo (Mica, SEM, Tomocube) and Computer Session
15:15 – 17:00 Practical Session 4 – Instrument Demo (Mica, SEM, Tomocube) and Computer Session
09:00 Introduction to EuroBioImagung
10:00 Practical session: 3D Slicer
12:00 Lunch Break
13:00 Practical Session 5 – Computer Session
14:30 Social Event – Josephinum
16:00 Workshop evaluation and final remarks
17:30 Farewell – Sägewerk
Dates & Information
Online part: 31.03.2023
On-site part in Vienna: 24.-26.05.2023
Medizinische Universität Wien
Zentrum für Anatomie und Zellbiologie
Seminarräume 4-6 (vorderer Eingang, 1. OG).