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. Read an interview with Romain here
- 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
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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.
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PC Cheng and Felix Margadant are contributing authors to the book 'Handbook of Biological Confocal Microscopy' available here.
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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, ilastik, Nikon NIS.
Full list of teaching faculties
- Rainer Heintzmann (Leibniz Institute of Photonic Technology in Jena, Germany)
- Felix Margadant (Radium Hospital, Oslo University Hospital, Norway)
- Kay Schink (Radium Hospital, Oslo University Hospital, Norway)
- PC Cheng (State University of New York in Buffalo, USA)
- Anna Klemm (UPPSALA University, Sweden)
- Rafael Camacho (University of Gothenburg, Sweden)
- Korbinian Bösl (University of Bergen,Norway)
- Guergana Dontcheva (Bitplane.com, UK)
- Laura Rodriguez de la Ballina (Riks Hospital, Oslo University Hospital, Norway)
- Dominik Frei (Inter Instrument As, Norway)
- Frode Skjeldal (IBV, University of Oslo, Norway)
- Maria Àngeles Jimènez Sigstad (NCMM, University of Oslo, Norway)
- Øyvind Ødegaard Fougner (Radium Hospital, Norway)
- Edna, Xian Hu (NCMM, University of Oslo, Norway)
- Pia Larsson (Australian Centre for Blood Diseases, Monash University, Australia)
- Stephen Cody (Monash Micro Imaging, Australia)
- Romain F. Laine (Ricardo Henriques group, MRC LMCB, University College London, UK)
- Bjørnar Sporsheim (NTNU, Norway)
- Niklas Boknäs (Linköpings Universitet, Sweden)
- Felix Wechsler (Leibniz Institute of Photonic Technology in Jena ,Germany)
Organizing Committee: Edna, Xian Hu; Oddmund Bakke ; Felix Margadant ; Kay Schink
Supporting Staff : Linda Haugen(IBV Invoicing), Elisa Bjørgo(NCMM Administration), Annabel Darby(NCMM Communication), Larissa Lily (NCMM Administration), Harold Gutch (NCMM IT) and Sabry Razick(UiO IT).
Due to server capacity for our lab sessions, the workshop can only host 70 participants. The registeration is closed as we have reached maximum capacity.
If you are interested to join the lectures please contact Annabel ( annabel.robertson at ncmm.uio.no) to receive the lecture zoom links.
Chart of distribution of registered students. A total of 7 students have been granted scholarship.
This workshop received financial support from Digital Life Norway and BNMI (NordForsk Research Infrastructure Hubs).
The student image processing server is supported by UiO Central IT.
Imaris and NIS server licenses are sponsored by Bitplane and Nikon.