6th NorMIC Imaging Workshop - Course in Advanced Light Microscopy and Image Processing
The NorMIC series of workshops aims to teach biological researchers (PhD students, postdocs and young PIs) the principles of biological microscopes and image processing.
Bioimaging has become a potent and popular tool for biological researchers. However, many biologists that regularly use imaging don’t fully understand the basic principles of how the technology works. This can cause issues as, unlike other techniques such as a Western Blot, mistakes made in bioimaging are not immediately obvious to the untrained eye. Correctly processing generated images can also cause issues if the researcher has not been properly trained.
The NorMIC series of workshops aims to teach biological researchers (PhD students, postdocs and young PIs) the principles of biological microscopes and image processing, and to educate them about the pros and cons of different types of microscopes and processing algorithms, alongside the potential artefacts that might come with using the technology.
The workshop, organised by NCMM and Oddmund Bakke, Department of Life Sciences, UiO will cover the basics of optical microscope image formation, common artefacts, image data management with regards to the FAIR data principle. All are taught with an emphasis on image processing. We will cover the key techniques used in image processing alongside the common tools that are either free for researchers to use or available at the University of Oslo and Oslo University Hospital’s shared facilities.
Teaching will come from world-leading researchers
- Rainer Heintzmann, the co-inventor of Structured Illumination Microscopy (SIM) and Instant Structured Illumination Microscopy (iSIM). Rainer will demonstrate the powerful free deconvolution software developed in his lab.
- Anna Klemm, an image processing scientist and well-known Cell Profiler instructor. Anne has trained many of the imaging specialists in Oslo. View some of her work here.
- Romain F. Laine, a researcher from the Ricardo Henriques group, the group that invented SRRF stream.
- Stephen Cody, of Monash Micro Imaging. Stephen is famous for generating many powerful online teaching tutorials for microscopy and several auxiliary live imaging tools.
- Felix Margadant, a member of the Harald Stenmark group. Felix has devised several cellular force measurement tools. A software suite used in his UiO collaboration is
PC Cheng, Professor at the Department of Electrical Engineering, State University of New York in Buffalo, USA and famous plant biologist. Specialist in confocal microscopy, biomedical imaging, x-ray microscopy, microtomography, and lithography.
PC Cheng and Felix Margadant are contributing authors to the book 'Handbook of Biological Confocal Microscopy' available here.
The topics that the course will cover include: image formation, processing workflow, segmentation, filters, de-convolution, rendering and visualization, classification, AI-based processing - see poster above for full details.
We will use the following software: Image J, Imaris, Cell Profiler, Nikon NIS, and Matlab.
Full list of teaching faculties involved:
- Rainer Heintzmann (University of Jena)
- Felix Margadant (Radium Hospital, Oslo University Hospital)
- Kay Schink (Radium Hospital, Oslo University Hospital)
- PC Cheng (State University of New York in Buffalo, USA)
- Anna Klemm (UPPSALA University)
- Rafael Camacho (University of Gothenburg)
- Korbinian Bösl (University of Bergen)
- Guergana Dontcheva (Bitplane.com)
- Laura Rodriguez de la Ballina (Riks Hospital, Oslo University Hospital)
- Dominik Frei (Inter Instrument As)
- Frode Skjeldal (IBV, University of Oslo)
- Maria Àngeles Jimènez Sigstad (NCMM, University of Oslo)
- Øyvind Ødegaard Fougner (Radium Hospital)
- Xian Hu (Centre for Molecular Medicine Norway (NCMM, University of Oslo)
Organizers: NCMM, Oddmund Bakke, Department of Biosciences (IBV), University of Oslo
Funding agents: Nordforsk, Digital Life.
Registration closes on the 24 May 2021.