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Industry Contest for young scientists
You are a young scientist, postdoc or junior professor in Germany, Austria, Switzerland or the Netherlands? You are working on an exciting cell biology project but do not have access to confocal high content imaging? The imaging part is missing for a step forward or your next publication?
Submit your imaging assay idea in the contest and win access to high quality results.
COMULIS Training School "Imaging Across Scales"
The five-day COMULIS Training School "Imaging Across Scales" took place at the University of Bern on September 4-8, 2023. Organized by Ruslan Hlushchuk, Benoît Zuber (Institute of Anatomy) and Yury Belyaev (Microscopy Imaging Center) this event offered a balanced mix of theory and hands-on experience for 9 students from 4 European countries.
The event started with a keynote talk by Stephan Handschuh of Vet-Med University of Wien on correlative workflow. Days 2 and 3 showcased diverse perspectives with speakers such as Ruslan Hlushchuk on uAngio CT, David Haberthür on uCT analysis, Paolo Ronchi from EMBL Heidelberg on X-ray tomography, and Benoît Zuber on SBF SEM. Industry views were presented by Phil Salmon from Bruker microCT and Emine Korkmaz from ThermoFisher Scientific. Joana Delgado Martins from University of Zurich discussed big data storage and handling.
Participants, divided into four rotating groups, took part in hands-on sessions covering uAngioCT sample preparation, uCT and EM imaging workflows and image processing. These sessions enabled a practical application of the topics discussed in the lectures and enabled participants a possibility of one-to-one communication with imaging experts.
The final day included group presentations and a feedback session, rounding off a week of comprehensive learning and networking, which also included a welcome dinner and a city tour. Overall, the program successfully fused expert talks, practical training, and networking activities.
The training school was supported by the Institute of Anatomy, Microscopy Imaging Center, and COMULISglobe - Chan Zuckerberg Initiative.
Summer Series 2023 from the Dubochet Center of Imaging
The Dubochet Center of Imaging (DCI) summer 2023 seminar series is an excellent opportunity to hear the latest in cryo-EM and cryo-ET from leading researchers in the field.
The next dates and speakers will be:
- Arjen Jakobi (TU Delft, NL) on 01.09.23, 12:00, at EPFL Lausanne (Cubotron, BSP231)
- David Barford (MRC LMB Cambridge, UK) on 15.09.23, 11:00, at Uni Geneva
- Florian Schur (ISTA Klosterneuburg, Austria) on 22.09.23, 13:15, at Uni Bern (Ewald Weibel Auditorium, Institute of Anatomy)
Please contact us if you would like to have any further information.
CEM Summer School 2023
From July 6th to 7th, 2023, the annual summer school of the PhD program Cutting Edge Microscopy (CEM) took place at the Seehotel in Bönigen, Switzerland. Bönigen is a beautiful village on Lake Brienz. All students gave scientific presentations on their projects, with a focus on the microscopy applied and the results obtained. Since the students’ projects cover very different topics and a broad variety of microscopy, a new structure was tried: For each session, groups of 2 to 4 students were formed depending on the type of microscopy used or their scientific project. To introduce and explain the microscopy, the students were encouraged to make joint presentations. This format encouraged a more lively atmosphere and was greatly appreciated by all participants. The even livelier review of the scientific part of the summer school took the form of a quiz in which each student contributed to a question pool covering all presentations. Advice on how to implement microscopy in the projects was provided by the MIC microscopy specialists Fabian Blank and Yury Belyaev, the MIC bioimaging specialist Guillaume Witz and the CEM PhD program co-directors Benoît Zuber and Steven Proulx. Ruth Lyck, the CEM PhD program coordinator, was responsible for the quiz and hotel organization. In addition to the scientific program, a discussion on upcoming activities of the CEM PhD program took place. As the new CEM students’ representatives Adrian Madarasz and Marwa Mangattu Parambil were elected. During their term from August 2023 until July 2024, Adrian will join the MIC committee as the students’ representative. Another much appreciated activity was the visit of Leica Microsystems representatives Annette Rinck, CEO, and Michael Weuffen, Service manager. The beautiful landscape, the pleasant accommodation and free time to swim in Lake Brienz or go jogging contributed to a perfect learning atmosphere.
ELMI 2023
The 22nd International European Light Microscopy Initiative Meeting place on June 6-9, 2023 in Noordwijkerhout, The Netherlands. More than 400 participants from Europe and the whole world discussed recent advances in light microscopy aimed at a life sciences audience.
During the first day of the meeting, in a traditional core facility session, the representatives of the imaging facilities discussed the topics of common interest such as cyber security, facility equipment maintenance and tools, staff development, data management. During the following two and a half days of the conference the leading scientists in the field presented and discussed with delegates the latest achievements in microscopy. The topics of this year were: Functional imaging, new technologies, data management & analysis, intravital & light sheet, CLEM, and high content. Additionally, more than 50 leading companies active in microscopy instrumentation and related fields introduced latest cutting-edge technical developments in informative workshops and booth presentations. As usual, ELMI provided an excellent opportunity for networking with colleagues from Industry and Academia.
MIC was well represented by three MIC members. Olivier Pertz (Institute of Cell Biology), Ruslan Hlushchuk (Institute of Anatomy) and Yury Belyaev (MIC) attended the meeting. Olivier gave an invited talk ‘’Spatio-temporal interrogation of signalling networks using biosensor imaging and optogenetics’’ covering the latest work in his lab. Ruslan in his talk ‘’Towards high accuracy µCT-LM-EM correlative workflow with fluorescent µCT contrast’’ presented along with the research of his group also a collaborative project with Yury Belyaev and colleagues from the University of Fribourg (Felix Meyenhofer, Boris Egger) and the University of Porto (Paula Sampaio, Ines Alencastre and Maria Azevedo).
Congratulations to successful PhD Defense Anastasia Milusev
On July 6, 2023, Anastasia Milusev, student at the PhD program Cutting Edge Microscopy (CEM) under the supervision of Prof. Dr. Robert Rieben and Dr. Nicoletta Sorvillo has successfully defended her PhD thesis with the title "Distinct arterial and venous glycocalyx dynamics impact endothelial function".
Abstract: The endothelial glycocalyx, a layer of sugars and proteins on the endothelial cell surface, is crucial for maintaining vascular homeostasis. The glycocalyx is damaged in different inflammatory conditions, leading to a pro-inflammatory and procoagulant endothelial cell phenotype. Using confocal microscopy and live cell imaging, the glycocalyx dynamics of arterial and venous endothelial cells in different inflammatory conditions were investigated in vitro in a 3D microfluidic system.
MIC Research Day 2023
On June 28, 2023, more than 120 participants from the University of Bern, Fribourg, Geneva, and industry representatives attended the traditional MIC research day, that took place at UniS. The well-balanced program of the event featured MIC users from all three Faculties of the MIC (Vetsuisse, Natural sciences and Medicine) as well as one researcher from the University of Fribourg and one industry speaker.
Nine scientists presented their research projects related to microscopy. Among them, Ora Hazak from the University of Fribourg introduced her studies of plant receptor-ligand signalling using fluorescence lifetime imaging. An industry representative, Nikolaos Droseros from GMP, informed the audience about the latest developments of lasers for multiphoton microscopy. Finally, two students who successfully graduated from the PhD program Cutting Edge Microscopy (CEM) received their certificates.
As usual, this event provided plenty of opportunities for networking among the imaging community at the University of Bern. We thank all CEM students for their help in the organization, all participants for their enthusiasm for microscopy and event sponsors for their generous financial support.
Inauguration Symposium for new electron microscopes at the Institute of Anatomy on July 5, 2023
The inauguration symposium to celebrate acquisition of the Titan Krios G4 transmission cryo-electron microscope and the Aquilos 2 cryo-focused ion beam milling scanning electron microscope takes place in the Ewald R Weibel Auditorium (Room No. A224) at the Institute of Anatomy, Bühlstrasse 26, 3012 Bern, on July 5, 2023. Prof. Werner Kühlbrandt of the Max-Planck Institute of Biophysics in Frankfurt will be sharing his insights in a scientific talk entitled “High-resolution cryoEM of mitochondrial membrane proteins”. Registration via e-mail to office.ana@unibe.ch.
Invitation to the MIC Research Day 2023
We are pleased to invite you to our annual MIC Research Day on June 28, 2023.
The MIC Research Day shows a selection of research highlights based on microscopic techniques that have been realized by scientists from the University of Bern. Junior and senior researchers who are specialists in microscopy present data on their exciting research projects, which were achieved using state-of-the-art microscopy. With this event, the MIC brings together scientists using microscopy with other researchers who may wish to use the same instrument or a similar technique.
We are happy to present a day full of interesting topics and discussions and we are honoured to welcome great speakers who will share their expertise on microscopy in their various research areas.
We are looking forward to welcome you in June.
Find all information and registration here.
Short term scientific mission in Porto, Portugal, by Dr. Yury Belyaev
In April 2023, Dr. Yury Belyaev, light microscopy manager of the Microscopy Imaging Center of the University of Bern, visited the Advanced Light Microscopy (ALM) and the Bioimaging scientific platforms at i3S - Instituto de Investigação e Inovação em Saúde, the University of Porto, Portugal. For this 5-day short-term scientific mission (STSM), Yury Belyaev received financial support from the COST (European Cooperation in Science and Technology) Innovator Grant COMULIS (Correlated Multimodal Imaging in Life Sciences) MultEMPlex IG17121.
The aim of STSM was to show a feasibility of implementation of super-resolution and lifetime microscopy into the existing micro computer tomography(µCT)/light microscopy (LM) correlative workflows at the University of Bern. The samples of mouse kidney from the µCT group of PD Dr. Ruslan Hlushchuk, Institute of Anatomy, University of Bern, were investigated using the Leica Stellaris 8 FALCON (FAst Lifetime CONtrast) STED (STimulated Emission depletion) confocal microscope. Different sample preparation protocols suitable for high-resolution STED imaging have been also tested.
The obtained results allow higher correlation precision with additional tissue specificity and possibility of label-free imaging in existing multimodal correlative workflows and open the possibility to develop it further in the direction of electron microscopy. The scientific outcome of STSM will be presented in one of the upcoming meetings on correlative multimode imaging. Finally, the visit has contributed to the development of scientific collaboration between Portugal and Switzerland.
The Grantee would like to thank COST Action for financial support and the members of the ALM and Bioimaging scientific platforms at the i3S institute for their hospitality, friendly atmosphere, and excellent scientific input during this STSM.
PhD Defense L. van Os
Lisette van Os, student at the PhD program Cutting Edge Microscopy (CEM) under the supervision of Prof. Dr. Olivier Guenat, will give her thesis defense on April 27, 2023.
Title: Immune cell migration during infection in organs-on-chip
Abstract: Organ-on-chip models aim at replacing traditional animal experiments in the research and drug development pipeline. Current organ-on-chip models can replicate the functional unit of an organ, but often do not include an immune component. In this project, an organ-on-chip model of lung infection was developed, to study immune cell migration during the acute infection phase. Live microscopy was carried out to follow the migration pattern of immune cells under different (inflammatory) conditions. Immune cell migration during lung inflammation could be visualized in real time.
PhD Defense S. Mutlu
Seyran Mutlu student at the PhD program Cutting Edge Microscopy (CEM) under the supervision of PD Dr. Fabian Blank and PD Dr. med. Amiq Gazdhar will give her PhD Defense on April 26, 2023.
Title: Adoptive transfer of HGF overexpressing T cells as potential therapeutic approach for bleomycin injured lung mouse model
Abstract: Idiopathic pulmonary fibrosis (IPF) is a lethal disease emerging from aberrant wound healing mechanisms disturbing the alveolar epithelial (AE) integrity. The immune system (IS) is known to be involved too. Hepatocyte growth factor (HGF) showed antifibrotic properties. We aim to study if adoptive transfer of HGF modified T cells (HGF-T cell treatment) in bleomycin injured mice (BLM model) may promote balancing of the pulmonary IS and repair of the AE.
We established a model of precision cut lung slices, which were analyzed by confocal microscopy in order to observed instillated T cells after treatment in the murine lung. Live-cell imaging was operated on co-cultures using the Incucyte system to see if HGF transfected T cells were interacting with myofibroblasts.
Congratulations to successful PhD Defense Daniëlle Verschoor
On February 10, 2023 Daniëlle Verschoor, student of the Cutting Edge Microscopy (CEM) program under the supervision of Prof. Stephan von Gunten, has successfully defended her PhD thesis with the title: “Granulocytes, fragile but resistant. Unraveling the treatment resistance of granulocytes.”
Her PhD project focused on the treatment resistant of inflammatory granulocyte, both neutrophils and eosinophils. Freshly isolated human peripheral granulocytes were stimulated with pro-inflammatory cytokines as GM-CSF and/or IL-5 followed by treatments as intravenous immunoglobulins, anti-siglec-7/9 or glucocorticoids to investigate their cell survival or death and to investigate possible mechanism involved in this response. In her project microscopy was used to characterize subsets of cells and analyze/visualize cell death. This all to unravel the mechanism responsible for their resistance to these treatments.
Fundamentals of wide field microscopy
The MIC Training "Fundamentals of wide field microscopy" will take place on May 09 - 11, 2023. Content of the course will be: Basics of wide field microscopy. Basics of fluorescence. Filters and light sources. Digital cameras and digital imaging. Basics of image visualisation and processing, deconvolution and denoising.
On request, PhD students of the Cutting-Edge Microscopy program can obtain 1.5 ECTS upon presenting the learning outcome in the context of their project at a presentation event.
Registration closes on May 2, 2023.
Detailed information and the registration form are to be found on ILIAS.
Demonstration Events
The InCell Analyser (INCA) high-throughput microscope at the Vetsuisse Faculty has to be replaced soon. To learn about the performance of instruments on the market demonstration events will be held for the Molecular Device (Nano/Micro) instrument on March 27-30 and for the Cytation 5 and 10 instruments on April 18-19, 2023. Please contact Prof. Kässmeyer, Dr. Kerry Woods or Dr. Helena Röss if you are interested in joining these demonstration events.
MIC Workshop: Performance Test in Light Microscopy
In collaboration with the Friedrich Miescher Institute for Biomedical Research in Basel, the MIC will offer the course “Performance Test in Light Microscopy”. It will take place on April 26-27, 2023. The course will present some basic performance tests to diagnose issues and benchmark performance of light microscopes. Please find all further information on the flyer below.
In case you are interested, please send your application to: yury.belyaev@mic.unibe.ch
Application deadline: March 10, 2023
CEM Study Trip 2023
In February 2023, a study trip took the PhD students of the PhD program Cutting Edge Microscopy (CEM) to Freiburg i.B., Germany. Here, the students visited the Life Imaging Center (LIC) of the University of Freiburg. The institute is headed by Dr. Roland Nitschke, who warmly welcomed the students and led them through the 2-day program together with his team. A relaxing tour through the beautiful city center of Freiburg i.B. completed the program. Read more about the study trip of the CEM PhD students to Freiburg in the pdf file linked below.
Advanced Imaging Course - UniFR
The Microscopy Imaging Center (MIC) collaborates with the Bioimage Core Facility of the Department of Biology and the Section of Medicine of the University of Fribourg. The course Advanced Imaging - Super-resolution fluorescence microscopy is open for PhD students of the Cutting Edge Microscopy specialization program.
Fluorescence microscopy has become the preferred imaging tool for biological systems due to its capability to visualize specifically the target biomolecules under conditions compatible with life, like room temperature, liquid environment and irradiation with visible light. Fluorescence microscopy also provides very high sensitivity down to the detection of single molecules. As drawback, as it happens with any a far-field optical technique, the spatial resolution is limited by the wavelength of light to a few hundreds of nanometres (the so-called diffraction limit). Remarkably, in the mid 2000s, a series of imaging methods using fluorescence readout were developed that deliver images with resolution beyond the diffraction limit. These methods, called super-resolution fluorescence microscopy or far-field fluorescence nanoscopy and whose pioneers were awarded with the Nobel Prize in Chemistry in 2014, have revolutionized biological imaging and continued to be developed until the present day.
Detailed information are to be found on ILIAS here. KSL: 482916
PhD Defense M. Golomingi
Murielle Koni-Kepo Golomingi student at the PhD program Cutting Edge Microscopy (CEM) under the supervision of Prof. Dr. Verena Schröder, will give her PhD Defense on March 15, 2023 at 14.00 at the ARTORG Center for Biomedical Engineering Research.
Title: “Interactions between the complement system and blood coagulation: a potential role of complement components and activation during haemostasis"
Haemostasis is a crucial process by which the body stops bleeding. It is achieved by the formation of a platelet plug, which is strengthened by the formation of a fibrin mech through the coagulation cascade. In case of pathological clotting, for instance in arterial thrombosis, the interactions of the complement system and the coagulation cascades is known to aggravate the development of the pathology. Whether those interactions play a relevant role during non-pathological haemostasis is however not yet completely understood. The aim of this study was to investigate the potential role of complement components and activation during haemostasis.
It is time to navigate your career maze!
The Life Science Zürich Young Scientist Network (LSZYSN) invites you to the Zurich Life Science Day, on the 7th of February 2023 at Irchel Campus. This is a day-long career fair and networking event with the most talented life scientists and companies.
The LSZYSN is a non-profit organization composed of PhD students and Post-Doctoral researchers from ETH and University Zurich. Our goal is to connect life scientists with their career opportunities beyond academia.
Over the last 12 years, the ZLSD has grown into the largest job fair for life scientists in Switzerland, hosting more than 700 participants and 100 company representatives on site at the Irchel Campus of the University of Zurich. Due to the Covid-19 situation we went virtual the last 2 years and hosted over 2000 participants from all over the globe, who connected with company representatives over informal 1-1 meetings, and numerous chatting options. However, ZLSD is back on campus and you get to do all networking in person.
Muldimodal Imaging
On February 2, 2023 the AGORA Cancer Research Center invites you to the workshop titled "Multimodal Imaging in life sciences and cancer research". Keynote speaker is Ralph Weissleder, Harvard/ MGH, USA. More details and registration on the pdf below.
SNSF Scientific Image Competition
Get your cameras and give Swiss research a face!
The SNSF Scientific Image Competition encourages researchers working in Switzerland to present their works to the public and the media. Photographs, images and videos will be rated in terms of their aesthetic quality and their ability to inspire and amaze, to convey or illustrate knowledge, to tell a human story or to let us discover a new universe.
Submission deadline is January 31, 2022. Learn mor here.
First protocol for Monitoring the point spread function
MIC congratulates Dr. Yury Belyaev on his co-authorship in a new publication on the use of the point spread function for quality control of confocal microscopes. The paper can be downloaded here.
Benchtop High-Speed Confocal Microscope
Yury Belyaev (MIC) and Fabian Blank (DBMR) invite you to this demonstration event organized in collaboration with Witec AG. More details and registration on the flyer below.
Congratulation to successful PhD Defense
On September 20, 2022 Raphaela Seeger, student of the PhD program Cutting Edge Microscopy (CEM) has successfully defended her PhD thesis entitled "Investigating synaptic vesicle exocytosis by structural studies of rat synaptosomes".
During this project synapses were isolated and treated with an exocytosis triggering solution prior to vitrification by plunge freezing to achieve a temporal resolution and investigate the morphofunctional changes in the synapses' architecture via cryo-electron tomography. In parallel, tomograms of synapses with a mutated exocytosis-relevant-molecule (SNAP25) from collaborators (University of Copenhagen) were evaluated and compared with the results of the time-resolved exocytosis events. Further, a deep-learning software to automate the segmentation of synaptic vesicles was created in a collaboration with another PhD student from the Zuber lab.
Swiss Microscopy Core Facility Day 2022
The 10th Swiss Microscopy Core Facility Day took place this year on September 15 - 16, 2022 and was organised by Pascal Lorentz from the Department of Biomedicine at the University of Basel. To celebrate the 10th anniversary, this normally one-day event, was organised as a two-day retreat in Engelberg. About 60 members of Swiss microscopy facilities and representative of different microscopy companies convened for informative presentations and intensive discussion on questions related to various aspects of microscopy faculty operation. The focus of this year’s meeting was the well-being of the facility staff.
On the first day, the leading microscopy companies shared their experiences in supporting good working atmosphere among employees. Additionally, Christel Genoud from the University of Lausanne presented the results of a facility survey on the working conditions of microscopy facility employees. On the second day, after Zeiss’ presentation of Zeiss on the latest developments in artificial intelligence (AI) software and Evident’s brief overview of corporate wellbeing issues, the participants were able to participate in variouse workshops. All workshops were led by professional coaches and gave an insight into modern psychological methods tackling questions of mental health, self-reflection and conflict management.
As usual, the meeting offered many opportunities for networking and exchange of experiences during its social program. Yury Belyaev represented the Microscopy Imaging Center (MIC) at this meeting. Next year the Swiss Core Facility Day will take place at ETH Zurich organised by ScopeM.
MIC at "Nacht der Forschung 2022"
The Nacht der Forschung at the University of Bern took place on September 10, 2022. The room of the microscopy imaging center (MIC), UniS A015, was decorated with various posters about the MIC and about microscopy at our University. Activities included "Microscopy for everyone" on 6 teaching microscopes and an excursion into virtual reality, which beamed the guest into the brain of a mouse or into a fish head. In room A-126 of UniS, microscopists offered lectures on exciting topics. A total of around 30 helpers from the MIC committee, friends of the MIC and students of the PhD program Cutting Edge Microscopy headed by Fabian Blank, Ruslan Hlushchuk and Ruth Lyck were on duty in 3 shifts from 4:00 p.m. to midnight. Further activities of MIC committee members were offered in the University’s main building by Stefan Tschanz and Benoît Zuber on behalf of the Institute of Anatomy. All activities were eagerly attended. Interested conversations and happy children's faces testified to the success of our offers. The MIC team says a big "THANK YOU" to all the helpers, without whom the MIC activities would not have been possible.
Scanning System VS200 and All-in-One Microscope APX100
This workshop, organized in collaboration with Yury Belyaev (MIC) and Fabian Blank (DBMR), will take place on October 5, 2022 at the Department for BioMedical Research, Bern. For further details please see the flyer below.
Entry-level position at the Imaging Core Facility (IMCF)
The Imaging Core Facility (IMCF) of the Biozentrum of the University of Basel is offering a position to a young scientist to enter the field of modern high-end light microscopy. More details see here.
Translational molecular imaging: Using a mass spectrometer as a microscope
The Department for BioMedical Research (DBMR) at the University of Bern is hosting Prof. Dr. Ron M.A. Heeren from the Molecular Imaging Institute, Maastricht University at the DBMR Research Conference.
The conference is taking place on October 31, 2022 at the Langhans Auditorium. More information here.
PhD midterm presentation by MD Adrian Madarasz
On December 16, 2022 at 2.00 pm. Title: “Circulation and clearance of cerebrospinal and brain interstitial fluid in murine models of hemorrhagic stroke". Location: Theodor Kocher Institute, University of Bern.
MD Adrian Madarasz is enrolled in the PhD program Cutting Edge Microscopy and conducts his thesis under the supervision of Dr. Steven Proulx at the Theodor Kocher Institute
Abstract of his presentation: Hemorrhagic stroke is associated with high disability and mortality rates. Most therapeutic approaches lack broad agreement, especially for the reduction of brain edema. By inducing disease models for intracerebral and subarachnoid hemorrhage in mice followed by in vivo imaging with near-infrared tracers and labels, we assess changes in brain interstitial and cerebrospinal fluid circulation and investigate potential efflux pathways for fluids and cells from the subarachnoid space.
Meet the MIC at the "Nacht der Forschung"
The MIC team invites the public to inspect fascinating specimen through a microscope, to see posters about the MIC and some microscopy examples done at the University of Bern and to enjoy 3D images in virtual reality in room A015. In addition, MIC experts will held presentations at 5.00, 6.00, 8.00, 9.00 and 10.00 pm in room A-126.
Workshop on Bioimage Processing with Python
From July 11 to 15, 2022, the 1st MIC Workshop on Bioimage Processing with Python, led by MIC team member Dr. Guillaume Witz, took place in the Bernese Oberland. A mix of eight participants from the University of Bern, three from European universities and one from a private company learned how to develop Python-based bioimage processing workflows using cutting edge tools like cellpose, napari etc. Participants also had the opportunity to work on their own projects and to discuss them with Guillaume Witz and with each other. It was a great experience to see how concepts and tools just taught were applied live to those projects, and how participants made massive progress in such a short time! During breaks and evening time the beautiful park of Sherlock Holme's favourite hotel in Meiringen was a wonderful stage for many more informal discussions on science, microscopy, biology etc. made especially interesting by the participants' diverse backgrounds. Finally, participants also enjoyed the many hiking and excursion possibilities available in Meiringen to recover from an intensive learning program. Inspired by this success, MIC will organize the 2ndMIC Workshop on Bioimage Processing in 2023. Stay tuned and visit our website for announcements!
CryoEM symposium - UHZ, Center for Micoscopy and Image Analysis
The UZH Center for Microscopy and Image Analysis invites to a mini-Symposium dedicated to the inauguration of the Titan Krios G3i on Monday, 3rd October 2022 at the Irchel Campus, University of Zürich. The Krios series represents cryo-transmission electron microscopes (TEMs) with atomic resolution. Therefore, this symposium could be helpful for you if you are dealing with TEM in your research projects.
Congratulations to an important research achievement!
Congratulations to Dr. Coralie Dessauges and the research group of Professor Olivier Pertz, Institute of Cell Biology, Faculty of Science, University of Bern, on the publication of their project "Optogenetic actuator – ERK biosensor circuits identify MAPK network nodes that shape ERK dynamics" in the EMBOpress journal Molecular Systems Biology in June 2022, downloadable at https://doi.org/10.15252/msb.202110670. In this work, Coralie and co-workers built circuits consisting of an optogenetic actuator to activate MAPK signaling with blue light and an ERK biosensor to measure single-cell ERK dynamics. The inducing light pulse is automatically provided by the microscope, allowing the simultaneous study of dynamic ERK responses in thousands of cells. In summary, this project improves our understanding on the MAPK signaling interactome.
CEM Summer School 2022
On June 30th and July 1, 2022, the annual summer school of the PhD program Cutting Edge Microscopy (CEM) took place at the Hotel Appenberg in Zäziwil, Switzerland. On the first day, the CEM PhD students presented their scientific projects and specific microscopic applications. Advice on the implementation of microscopy into the projects was provided by the MIC microscopy specialists Fabian Blank and Yury Belyaev, the MIC bioimaging specialist Guillaume Witz and the CEM PhD program co-directors Benoît Zuber and Steven Proulx. Furthermore, a discussion on the next activities of the CEM PhD program took place and Javier Pareja and Adrian Madarasz were elected as CEM student representatives from August 2022 to July 2023. On the second day, the external trainer Michael Berndonner carried out a very intensive training course in scientific presentation techniques. Moderation skills were also included in this course as an important topic for scientific conferences. The coordinator of the CEM PhD program, Ruth Lyck, also attended the CEM summer school and took care of all administrative issues. The beautiful landscape, the pleasant accommodation and the Appenberg games activity contributed to a perfect learning atmosphere.
Enabling imaging across scales
The First EMBL Imaging Centre Symposium ‘’Enabling imaging across scales’’ took place on May 31, 2022 at EMBL Heidelberg, Germany. At this meeting, Dr. Yury Belyaev represented the MIC and here reports about it.
21st International European Light Microscopy Initiative Meeting (ELMI)
The 21st International European Light Microscopy Initiative Meeting (ELMI) took place on June 7-10, 2022 in Turku, Finland. At this meeting, Dr. Yury Belyaev represented the MIC and here reports about it.
CEM Study Trip
In May 2022, a study trip took the PhD students of the PhD program Cutting Edge Microscopy to Strasbourg, France. Here, the students visited the Institute de génétique et biologie moléculaire et cellulaire (IGBMC). A relaxing tour through the beautiful center of Strasbourg completed the program. Read more about the workshops at the IGBMC on the pdf file below.
ZEISS Workshop online or in Basel
A Workshop dedicated to Tissue Clearing is jointly organized by The Imaging Core Facility (IMCF) of the Biocenter of the University of Basel and Zeiss on July 11 to 13, 2022
You will get the chance to explore this technology in different lectures in Basel or online. Specialists for ECI Clearing, Cubic Clearing and Smart Clearing will share their experiences. In the second part we will host a hands-on workshop, where you can carry out a selected clearing technique yourself. Further information here.
COMULIS training school "Imaging Across Scales"
29 August - 2 September 2022, Bern, Switzerland
The Microscopy Imaging Center and the Institute of Anatomy are organising a COMULIS training school ‘’Imaging across the scales’’ on 29 August – 2 September 2022 in Bern, Switzerland. This is a 5-days in-presence course with 16 participants. The talks and hands-on sessions will cover uCT-EM workflows. The course main topics are: uAngioCT, uCT and EM sample preparation, multimodal imaging, and image processing. Registstration here.
Mica microscope workshop at the Institute of Pathology
22nd -23rd June, 09:00-18:00 CET
It is our pleasure to invite you to book your personal demonstration of Mica - the world's first Microhub – hosted by the University of Bern at the Institute of Pathology. Discover true simultaneous 4-color widefield, confocal resolution and AI-supported analysis united in a sample-protecting incubator. All with a single push of a button!
Mica is a whole new way to do microscopy. Here’s why…
- Access for all
Automatic selection and optimization of imaging settings simplifies your experiment set-up and increases reproducibility - No constraints
Visualize 4 colors simultaneously in widefield and then switch to confocal without ever moving your sample. Select the right modality in real time - Radically simplified workflows
Intelligent automation and AI-supported analysis enables greater efficiency and a faster track to publication
Contact us to book a time for your live demonstration and have your questions answered.
Where: University of Bern, Institut für Pathologie, L570, Murtenstrasse 31, 3008 Bern
If you are not available during this time, please write an E-Mail.
First meeting of the Swiss BioImage Analyst's Society
June 22, 2022
Do you analyse images of biological samples? Do you provide such analysis as a service in an imaging facilty or a lab?
If yes, register at the first meeting of the Swiss BioImage Analyst's Society for an informal day of exchange.
Swiss TriM Scope and Ultra Microscope User Meeting
Welcome to the Swiss User Meeting taking place on June 28, 2022. For program and registration please see flyer below.
Open position as Analyst / Microscopist
The Center for Microscopy and Image Analysis at the University of Zurich offers a 4 year position. Further details see here.
11 - 15 Jul 2022: MIC Workshop on Bioimage Processing
If you want to get started using the Python eco-system for your bioimaging projects this intensive one-week workshop is the right thing for you. In addition to course time, you will also have some time to work on your own projects, just getting started or continuing an existing one, and will be able to discuss them with other participants and the instructor. PhD students of the GCB profit from a reduced price. More details on the pdf below, registration here.
Whole day live demo at DBMR Bern
A Revolutionary Approach to Detect, Characterize & Screen
Confocal+ Widefield + Multimode Reading= Stunning Images+ Analysis
Join us for an overview of BioTek's new, next generation Cytation instrument, the Cytation C10 Confocal Imaging Reader.
We' ll highlight workflows to obtain phenotypic and quantitative data across its broad application range . Registration here.
Artificial intelligence methods applied to intravital microscopy of the immune system
This hyprid workshop will cover theoretical and practical aspects regarding the application of new A.I. -based methods for the analysis
of migration and interaction of immune cells captured by 4D intravital imaging. Basic knowledge in imaging is recommended.
More information and registration here.
LS2 Prestige Webinar
MIC committee member Benoit Zuber, as part of the LS2 Biophysics section, invites you to the upcoming LS2 Prestige Webinar.
Topic: “CryoEM structures of amyloid filaments from human brain”
When: 30th March 2022, 16:00 – 17:00 (CET)
Please register here.
Join the Cutting Edge Microscopy PhD program
Interested in becoming a world-class expert in biological imaging?
The CEM PhD program currently has a few vacancies. If you are a PhD student of the GCB and you apply advanced microscopy techniques in your PHD thesis, we are looking for you. Please find more details on the flyer below and do not hesitate to contact us.
Midterm presentation
Irene Spera, student of the PhD program Cutting Edge Microscopy (CEM), will give her midterm presentation on March 9, 2022 at 11:00 online via zoom. Title: "Factors regulating the exchange of cerebrospinal fluid and interstitial fluid of the brain".
Our project investigates the perineural outflow pathways of cerebrospinal fluid (CSF) at the cribriform plate and focused on the elucidation of anatomical connections between the subarachnoid space (SAS) and the lymphatics at the exiting nerve routes. Furthermore, we want to define the anatomical spaces of the CSF flow on the brain surface and elucidate the relationship between CSF and the interstitial fluid (ISF) of the brain. To address these aims, we made use of transgenic reporter mice, fluorescence microscopy, and through skull near-infrared (NIR) in vivo imaging.
Please request acess to this online event via e-mail to Rahel Eyer.
Join the Correlative Microscopy Symposium
March 13 - 16, 2022
The Organization Committee and the ZEISS Microscopy Team are delighted to invite you to the 6th Joint Meeting Workshop and Symposium “From 3D Light to 3D Electron Microscopy” taking place from March 13th to 16th 2022 in cooperation with the EMBL in Heidelberg, the VIB in Ghent and the Francis Crick Institute in London.
Many prominent scientists will share their groundbreaking work on correlative microscopy in 3D and volume EM. You can also look forward to practical workshops on
- correlative workflows
- volume EM methods
- sample preparation methods
and on a panel discussion of the international networking happening to promote these techniques.
This meeting will inspire you and open up the possibilities for forming new collaborative efforts to use these powerful imaging techniques to better understand the nano-world inside cells and tissues.
Please register here.
DCI Symposium 2022
The Dubochet Centre for Imaging (DCI) Symposium 2022 will take place in Lausanne and in Geneva June 8 to 10. More details and registration here.
Image analysis expert
The Friedrich Miescher Institute für Biomedical Research (FMI), Basel, is looking for an image analysis expert.. Please submit your application by February 25, 2022. For more details see the Job add below.
SNSF Scientific Image Competition
The SNSF Scientific Image Competition encourages researchers working in Switzerland to present their works to the public and the media. Photographs, images and videos will be rated in terms of their aesthetic quality and their ability to inspire and amaze, to convey or illustrate knowledge, to tell a human story or to let us discover a new universe. Submission deadline January 31, 2022. More information here.
PhD Defense
Federico Saltarin student ot the PhD program Cutting Edge Microscopy (CEM), will give his PhD defense on December 10, 2021 at 10.30 online via Zoom.
Title: “Investigations on the extravasation of melanoma cells across the blood brain barrier”.
Please request access to this online event via e-mail to Rahel Eyer.
Our project focuses on the investigation of the extravasation of melanoma cells across the blood brain barrier in the context of brain metastasis development.
To this aim, we addressed the impact of compromised endothelial junctions at the BBB on brain metastatic melanoma cell extravasation and we developed methods and tools for the investigation of melanoma brain metastasis formation on multi-scale level.
MIC Symposium 2021
Finally, after a missing year 2020 due to covid pandemic, the traditional MIC Symposium took place in UniS on November 19, 2021. The topic of this year was 3D electron microscopy. The scientific committee represented by Wanda Kukulski, Michael Stoffel, Benoît Zuber (University of Bern) and Dimitri Vanhecke (University of Fribourg), prepared an interesting program, which attracted more than 110 participants. More details see here.
LS2 Intersection Microscopy
The LS2 Intersection Microscopy together with the Swiss Society for Optics and Microscopy (SSOM) was founded in February 2019. During the past years, microscopy techniques as well as image analysis capabilities have developed at incredible pace. Today, microscopy based research is becoming increasingly important in all fields of life sciences. The LS2 microscopy intersection aims for a better and intensified knowledge transfer between the microscopy community and life scientists in Switzerland and thus intends to promote the faster introduction of new and cutting-edge microscopy techniques in Switzerland. Also, high-end microscopy techniques should become even better known as well as the core facilities providing them.
Apply for the LS2 membership here and select "Microscopy" in the online application form.
PhD Defense
Martin Liptay student ot the PhD program Cutting Edge Microscopy (CEM), will give his PhD defense on October 1, 2021 at 15:00 online via Zoom.
Title: “Replication fork remodeling and PARP inhibitor resistance in Brca1/2-mutated mouse mammary tumors”.
Please request access to this online event via e-mail to Rahel Eyer.
Poly (ADP-ribose) polymerase inhibitors (PARPi) are a class of targeted therapeutics that recently entered the clinic for the treatment of patients suffering from BRCA1/2-mutated breast and ovarian cancer. Unfortunately, similar to other anticancer therapeutics, their efficacy in tumor eradication is frequently limited by acquired drug resistance. By employing a variety of molecular biology and imaging techniques, we identified novel, non-canonical functions of DNA repair proteins H2AX and MDC1 in the metabolism of replication forks and in mediating PARPi response in BRCA1/2-deficient mammary tumors.
Zietschmann-Preuss-Award 2021
The 2021 Zietzschmann-Preuss Award presented by the World Association of Veterinary Anatomists goes to Christina Alexandra Kalenberg, Department of Clinical Veterinary Science, University of Bern, post-graduate student of MIC Board member Michael Stoffel. We congratulate her on this success!
Communication training for students of the PhD program Cutting Edge Microscopy (CEM)
The communication training for CEM students took place on 6 and 8 September 2021 in Berne. During two interesting and varied days, the participants had the opportunity to work on impactful speaking techniques, exercices for voice warming and were able to improve their personal skills under instruction of Michael Berndonner, external public speaking and communication trainer.
PhD Defense
Eleonora Lupi, student ot the PhD program Cutting Edge Microscopy (CEM), will give her PhD defense on September 29, 2021 at 15:30 online via Zoom.
Title: “Establishment of a zebrafish screening assay for the identification of compounds affecting proepicardial and epicardial formation”.
Please request access to this online event via e-mail to Rahel Eyer.
Description: the epicardium is the most external layer of the heart that has been demonstrated to have an important role during heart formation and regeneration. Despite the increasing interesting on this tissue, some mechanisms leading its formation remain still unknown. With this project we aimed to study the effect of epigenetic modulators on the proepicardial and epicardial formation in zebrafish model, to better understand the epigenetic role in this process. A drug screening was performed and zebrafish embryos were imaged using an Acquifer imaging machine. We were able to implement an automatic pipeline to quantify the number of the epicardial cells and determine the effect of the drugs on the epicardium.
PhD Defense
Alberto Mattei, student ot the PhD program Cutting Edge Microscopy (CEM), will give his PhD defense on September 1, 2021 at 10.00 am online via Zoom
Title: "Exploring Signaling Mechanisms regulating genetic and non-genetic Drug Resistance in Melanoma"
Please request access to this online event via e-mail to Rahel Eyer.
"Metastatic melanoma is a very aggressive type of cancer that in over 50% of cases carries a BRAFV600E mutation. The mutated BRAF drives aberrant MAPK-ERK pathway activation and tumor progression. Selective BRAFV600E inhibitors have been on the market since 2011, but drug resistance almost invariably develops and patient relapse in the clinic. We explored mechanisms that regulate genetic and non-genetic drug resistance in melanoma."
Congratulations to new publication!
Congratulations to Yury Belyaev, Federico Saltarin, Ruth Lyck and Paolo Favaro from University of Bern and their collaborators to their new publication on "Learning to Reconstruct Confocal Microscopy Stacks From Single Light Field Images" published in IEEE Transactions on Computational Imaging in July 2021, DOI.
Swiss Microscopy Core Facility Day 2021
Registration for the 2021 Swiss Microscopy Core Facility Day at the new Biozentrum in Basel is open.
Link to registration here.
LS2 Webinar Series
The LS2 Microscopy Intersection is happy to organise the LS2 Microscopy Webinar Series. One Tuesday each month, a speaker will share their exciting work on imaging methods and their applications in science or industry.
The next LS2 Microscopy Webinar will take place on the 20th July 2021 at 17:00 (~30min plus Q&A time). Register here.
ZEISS Microscopy Image Contest 2021
We are thrilled to announce the ZEISS Microscopy Image Contest 2021. Do you take stunning microscopy images? Submit your best image now! The contest is open to all microscopy enthusiasts and professionals in any application field. Images can be taken with any ZEISS microscope (light, X-ray or electron microscope). Deadline for entry is July 31, 2021.
All participants will receive a copy of the ZEISS Microscopy Calendar 2022. On top of that, the three winners will receive the following prizes:
- 1st Prize: ZEISS Primostar 3
- 2nd Prize: ZEISS Victory Pocket 10x25
- 3rd Prize: ZEISS Terra 10x42
To submit your image and read all FAQs and rules, visit our contest web page
New position in microscopy at Wyss Center, Geneva
The position is conceived to focus on transversal activities among the different microscopes and image analysis systems with technical roles on maintenance, assistance and quality control of the microscopes and integration of image analysis pipelines. The person will also be involved in the run of Wyss Center driven research projects.
Deadline 23th of July, with possibility of extension.
Exciting publication of Professor Olivier Pertz
We congratulate MIC committee member Oliver Pertz and his team to their exciting new study “Collective ERK/Akt activity waves orchestrate epithelial homeostasis by driving apoptosis-induced survival” published in Developmental Cell in June 2021.
QUAREP-LiMi WG 10 Image Quality Talk from Alan C. Bovik
"On Picture Quality Prediction"
Alan Bovik is a faculty member in the Department of Electrical and Computer Engineering, the Wireless Networking and Communication Group (WNCG), and the Institute for Neuroscience. His research interests include digital television, digital photography, visual perception, social media, and image and video processing. To recieve the Zoom link to this talk, please contact Yury Belyaev.
15th EXCITE Zurich Summer School
Registration is now open for the 15th EXCITE Zurich Summer School on Biomedical Imaging that will take place in Zurich, Switzerland, from 6 - 17 September 2021. Application deadline: Monday, 3 May 2021 (Notification of acceptance: 1 June 2021).
PhD Defense
Coralie Dessauges, student ot the PhD program Cutting Edge Microscopy (CEM), will give her PhD defense on May 3, 2021, at 1.00 pm. Title: An optogenetic actuator/biosensor circuit for large scale interrogation of MAPK signaling dynamics
Please request access to this online event via e-mail to Rahel Eyer.
In this work, we developed a set of optogenetic circuits to activate the MAPK/ERK pathway with light from different levels of the MAPK network and measure the corresponding ERK activity with a high temporal resolution. Together with automated imaging and image-analysis pipelines, our systems enable us to image and stimulate ERK signaling in hundreds of cells in a highly automated and dynamic fashion. Taking advantage of this throughput, we conducted an RNAi perturbation screen to investigate the role of 50 proteins of the MAPK network in ERK signaling regulation.
PhD Defense
Nora Ruef, student ot the PhD program Cutting Edge Microscopy (CEM), will give her PhD defense on March 26, 2021, at 4.00 pm. Please request access to this online event via e-mail to Rahel Eyer.
"In this thesis we investigated the unique migration mode of submandibular salivary gland tissue resident memory CD8+ T cells and how memory CD8+ T cells perform homeostatic surveillance of a complex organ with mixed epithelial – connective tissue composition."
PhD Defense
Julia Bruggisser, student of he PhD program Cutting Edge Microscopy (CEM), will give her PhD defense on March 25, 2021, at 3.00 pm. Please request access to this online event via e-mail to Rahel Eyer.
Title: Clostridium Perfringens β-Toxin: Receptor Identification and Oligomer Structure
Self-evaluation of the Microscopy Imaging Center (MIC)
Please complete the survey of the MIC here until March 16, 2021. This survey is designed to evaluate the performance of the MIC with respect to teaching and services. Your participation will help to implement improvements exactly there where you requested them most
New instrument at ARTORG
02.02.2021 - The newly acquired EVOS M7000 microscope from Thermo Fisher is a widefield fluorescence microscope, suitable for.... continue reading
White Paper of QUAREP-LiMi is online
29.01.2021 – Read the White Paper «QUAREP-LiMi: A community-driven initiative to establish guidelines for quality assessment and reproducibility for instruments and images in light microscopy» here.
Virtual Seminar Invitation - ImageXpress Pico
02.03.2020 - When size doesn't matter: meet ImageXpress Pico, the miniature but mighty microscope. Continue reading
DBMR Hyperion Imaging System
02.11.20 – New MIC Instruments
Location: INO-F608A
Type: Imaging mass cytometer
Site: UniBE-Insel Read more
DBMR Helios Mass Cytometer
07.10.20 – New MIC Instruments
Location: INO-F608A
Type: Mass Cytometer
Site: UniBE-Insel Read more
DBMR Hyperion Imaging System
05.10.20 – New MIC Instruments
Location: INO-F608A
Type: Imaging mass cytometer
Site: UniBE-Insel Read more
LHEP Keyence VHX-7000
05.10.20 – New MIC Instruments
Location: Gebäude der exakten Wissenschaften (ExWi)
Type: Widefield Microscope
Site: UniBE-ExWi Read more
IZB Nanolive 3D Cell Explorer
10.08.20 – New MIC Instruments
Location: Institute of Cell Biology, Baltzerstrasse 4, 3012 Bern
Type: Widefield Microscope
Site: UniBE-Muesmatt Read more
IRM ThermoFisher Phenom XL Scanning EM (Bob)
02.11.20 – New MIC Instruments
Location: Institute of Forensic Medicine, Bühlstrasse 20, 3012 Bern
Type: Electron Microscope
Site: UniBE-Muesmatt Read more