The NorMIC series of workshops aims to teach biological researchers (PhD students, engineers, postdocs and young PIs) the principles of biological microscopes and image processing.Time and place: Nov. 16, 2021–Nov. 19, 2021, ZOOM Add to calendar
Bioimaging has become a potent and popular tool for biological researchers. However, many biologists who 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 readily obvious to the untrained eye. Correctly processing recorded images can hence cause issues if the researcher has not been extensively trained.
The NorMIC series of workshops aims to teach biological researchers (PhD students, postdocs, and young PIs) the principles of biological microscopy and image processing, and to educate them on the pros and cons of different types of microscopes and processing algorithms, and introduce them to the potential artifacts inherent to 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 artifacts, and many popular state of the art imaging techniques (SMLM, SIM, expansion microscopy, 2P imaging, FRET, FRAP etc). All are taught with an emphasis on image processing. We will cover the key techniques used for 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.
With the revolution of bringing 3D printers to the masses, people have started getting creative in manufacturing and at home. These devices find their way into scientific areas, where researcher can fabricate customized labware in order to make everyday lab life easier. The apparent variety of types of printers and properties of printing materials might be intimidating for beginners. In this special edition of the NorMIC workshop, we will spend a few lectures covering the knowledge required to start 3D printing in your own laboratory.
In the last years, the open community of microscopy started putting efforts into making cutting-edge microscopes available to everybody by making use of 3D printers in combination with sharable CAD designs, Raspberry Pi cameras, and low-cost objective lenses. The second part of the 3D printing session in this workshop will give you an overview of what is there, how you can find resources to replicate and get your hands “dirty” while designing some parts for your microscope. Ultimately, we will show you how the open-source modular optical toolbox “UC2” (https://github.com/openUC2/UC2-GIT) can help you making your biological imaging experiments as easy as using a Fiji plugin.
Tentative Program of the Workshop
Registeration Deadline 10th Nov
The hands on session of the course is designed for 25 candidates. The registration fee will be 500 kr per participant. Lectures are open to public, email xian.hu at ncmm.uio.no for links for lectures.
More questions regarding the workshop? email xian.hu at ncmm.uio.no
Teaching will come from world-leading researchers as well as local imaging experts
- Professor Markus Sauer. Markus is actively researching in microscopy for early detection of diseases. He has extensive research experience on spectral resolution of single molecule and his most famous for the development of dSTORM (an important branch of Single Molecule Localization Microscopy). Markus is also one of the first adopters of Zeiss SIMsquard algorithm. Markus will share the most recent development of Expansion Microscopy(eXM) in his lab.
- Professor 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.
- Benedict Diederich, inventor of UC2, a low-cost 3D printed open standards microscope. Benedict and his colleagues have run a pilot workshop on UC2 in UiO in early 2020, now he’s back with an updated version of UC2 and valuable experience on 3D printing for lab equipments.
- Haoran Wang, PhD student of Rainer Heintzmann’s lab. Haoran has joined the UC2 3D printing project team a few years ago and will help Rainer and Benedict with the 3D printing part of our workshop.
- 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 https://imagej.net/PillarTracker.
- 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
- Kay Schink, Senior Research Scientist from Radium Hospital, Norway. Kay has extensive experience in various optical microscope techniques
- Ronen Zaidel-Bar, Professor of Tel Aviv University. Ronen will tell us how his group applied various imaging modalities on studying the mechanobiology of C.Elegans.
- Rafael Camacho, Imaging Scientist at University of Gothenburg. Rafael is a very active imaging processing specialist in Europe. He usually teaches ImageJ in our workshops and is well-loved by our previous students.
- Mingxi Yao, Assistant Professor in SuSTech. Mingxi has been studying the mechanosensing Ion channel Piezo1 with TIRF microscopy in the last few years, before Piezo1 won the Nobel Price this year(2021). He is also an expert in AFM and optical tweezers.
- Donato Sardella, A talented PHD student from Aarhus University. Donato has a fascinting success story of 2 photon kidney imaging in live mice to share. He has combined a self designed 3D printed imaging mount and an open source machine learning algorithm to overcome multiple challenges he has encountered.
- Guergana Dontcheva, Senior product specialist from Oxford Instrument.
- Dominik Frei, Senior product specialist from Inter Instrument.
Organizing Committee:
Edna, Xian Hu ; Felix Margadant ; Kay Schink ; Oddmund Bakke
Supporting Staff : Larissa Lily (NCMM Administration),Elisa Bjørgo (NCMM Administration), Harold Gutch (NCMM IT) and Sabry Razick (UiO IT), Linda Haugen (IBV Invoicing)
Link to past UC2 Workshop in UiO
Organizing Institutes:NCMM and NorMIC Imaging Platform, IBV
This workshop received financial support from Digital Life Norway , UiO:Life Sciences and BNMI (NordForsk Research Infrastructure Hubs).
The student image processing server is supported by UiO Central IT.
The Imaris student image processing Virtue Machines are provided by Oxford Instruments.
