2020 – Page 3 – The Live Cell Imaging facility

One-step non-toxic clearing protocol

Do you know that clearing is not just about light sheet microscopy? Even if you have done your job well and your sample is directly on the coverslip (not on the slide), as soon as your sample is thicker than 10 um (1 cell diameter), you will see the effect of the refraction index mismatch.

What is that? Your sample and the mounting medium around it have a certain refraction index (or likely several). The objective you are using is designed for a certain refraction index (e.g. air, water or oil). If these refraction indices do not match what happens? as soon as you image a tiny bit away from the coverslip, the sample will look elongated, the intensity and contrast will drop very fast.

Sounds familiar? If yes, changing your mounting medium to match the objective will solve the problem. It works for light sheet but it also works for wide field or confocal imaging! Just change your mounting medium and you will see an enormous difference!

Here is an article describing a one-step clearing protocol. This basically is about using a different mounting medium. Easy, cheap and non-toxic! Give it a try!

Have a look at this post for more info.

Broadcasted lectures from the LCI microscopy course and private demos of light sheet and cameras

Our course starts tomorrow! 😀

Target audience:

The aim for this course is to improve the microscopy skills of students and researchers who have already used a microscope to acquire digital images of fluorescent samples and want to improve their skills.

Registrations are closed but all lectures are open to everyone without registration.

The schedule and details of the venue are here.
All lectures are also available online live. The link and instructions to watch are here.
Make sure you check the schedule in case of last minutes changes.

If you are in Sweden, you are welcome to try some of the equipment on demo with your own sample.

To book at timeslot, please contact the responsible person directly.

Light sheet microscope from M2Lasers: Valentina Loschiavo Valentina.Loschiavo(at)m2lasers.com
- Fast imaging of large sample
- Overview function to navigate in the sample and find the region of interest
- 800x800um field of view with 1um min resolution
- Any immersion media
- Sample size up to centimetres
Wide Field microscope from Nikon with 3 different Andor cameras: Oliver Garner (oliver.garner(at)bergmanlabora.se)
- Nikon Ti2 microscope with 4 times larger field of view
- A front illuminated sCMOS camera: Good sensitivity and resolution, great speed, but a greyish background (Andor Zyla 4.2)
- A back-illuminated EM-CCD camera: highly sensitive camera with very dark background, but lower resolution and lower speed (Andor 897U)
- A back-illuminated sCMOS camera: same sensitivity and low background as an EM-CCD but better resolution and speed (Andor Sona)

The antibody validation nightmare

Ever wondered if that antibody you used throughout your whole PhD was actually also binding to something else than its supposed target protein?

Antibody validation in tissue staining is a very difficult task!

Here is a great step-by-step validation protocol published by EuroMabNet, a network of scientists who try to improve antibody validation.

And this paper gives a useful flow chart for antibody validation.

And here is the 5 pillars of antibody validation paper which explains what can be done to validate antibodies.

Know your RRid!

Imagine starting a study about some cool protein.

You find some useful articles on Google Scholar. In one paper, an antibody is mentioned. The name of the company that sold it to the authors is mentioned in the Material and Method but unfortunately that company has closed down or has been swallowed by one of the Pharma giants so you cannot order. Then you realize that the company was not producing any antibodies anyway, they were buying it from another company so there is no way to trace and buy the same antibody. Nightmare…

Then imagine that instead, the paper mentions the RRid number for that antibody. You do not know about what that is but you check and find this paper that explains it all.

Now suddenly, not only you can find on the Scicrunch website which company produces this antibody and which resells it so you can buy it, but you can also search pubmed for the RRid and find all the articles that mention it, opening your eyes to lots of results about your protein that have been published specifically with using that antibody. Now you can also check if the antibody gives consistent results!

And imagine being to do this for your favorite mouse model as well. See all publications that have mentioned your mouse RRId!

But it relies on you writing the RRid of your antibody or mouse in your next publication so think about it! 😀

Transfecting hard-to-transfect cells

Here you can see a nice film of a beating cardiomyocyte.

It was transfected using Fuse-it vesicles full of the mRNA of LifeAct-tagGFP2. According to Ibidi, it also work well with primary cells which are typically difficult to transfect.

RNA-based transfection seems to be gaining speed compared to classical transfections using DNA.

If you try it, leave some comments here to tell us how it worked for you! 🙂

Great video Microcourses about microscopy

Jennifer Watson’s Microcourses channel on You Tube is really recommended to anyone who uses a microscope.

Short targetted videos that will boil down the principles of light microscopy for biologist and help you understand what you are doing.

There are a few series, each of them with a few videos and the collection is constantly growing. Remember to subscribe so you get to know when they post a new one.

New image analysis training school with Neubias

NEUBIAS, the Network of European BioImage Analysts, is delighted to announce two new Training Schools on BioImage Analysis:

TS14 for Early Career Investigators (Life Scientists: PhD candidates, Postdocs, Staff, …):

This training school will cover the basics of image analysis using ImageJ/Fiji, as well as image analysis workflow automation using ImageJ macro programming. In addition, it will be taught how to use the software package ilastik for machine learning based image segmentation and object classification, and how to integrate ilastik into ImageJ macro based workflows. Moreover, an overview of further relevant bioimage analysis software packages will be given and there will be ample time for “Work on Your Own Data” sessions assisted by experienced Analysts.

TS15 for BioImage Analysts (advanced level):

This school targets bioimage analysts, who are willing to enhance their professional scope and techniques for improving the quality of their analysis, at the same time as willing to contribute with their knowledge and experience to the school. Prerequisite is a proficiency in at least one programming language (we do not train coding). The school focuses on workflow designing. This year, we will have a particular emphasis on statistics for bioimage analysis and related tools e.g. R and Python libraries. In addition, we will overview machine & deep learning components.

The schools will be held in Bordeaux, Feb 29 – Mar 03 2019, hosted at the Centre Broca Nouvelle-Aquitaine by the Bordeaux Imaging Center (BIC) and the Interdisciplinary Institute for Neuroscience. The selected students will be able to attend the whole NEUBIAS conference as part of the training.

NEUBIAS schools are an excellent opportunity to learn from many experts in Bioimage Analysis (we are expecting >20 specialists at the event) and “…a great mix of intensive learning and community networking” (former trainee testimonial). All schools include practical sessions “Work on Your Own Data”, plenary seminars and a session on ethics in image analysis.

Applications are now open (TS14 = 25 seats, TS15 = 35 seats and ~10+ trainers per school). Within the COST framework (funders of NEUBIAS), we will offer up to 7 travel grants per school to applicants who qualify.

Application deadline: December 12th 2019 Selection notification: December 20th 2019

More information about schools (programme & trainers) and venue, travel & lodge available at our website:

eubias.org/NEUBIAS/training-schools/

eubias.org/NEUBIAS/training-schools/eci/ts14-bordeaux-2020/

eubias.org/NEUBIAS/training-schools/analysts/ts15-bordeaux-2020/

We kindly ask that you help us reach out to all potential interested applicants.

on behalf of all NEUBIAS members, local organizers (Florian Levet and Fabrice Cordelières), scientific organizers (Romain Guiet, Elnaz Fazeli, Christian Tischer, Kota Miura, Marion Louveaux), and NEUBIAS Training Leaders Gabriel Martins and Fabrice Cordelières.

Apply now to the LCI microscopy course 2020 :)

It is now time to register to the LCI intensive microscopy course (Jan/Feb 2020). Check out the course schedule.

Loads of fun workshops, informative lectures, intense discussions and our popular Student Imaging Challenge workshop where students get direct feedback on how to improve their own sample preparation/experimental design.

We always run two courses in parallel:

the full course (#2870, 6 points, apply here) where students attend all activities
the theory only course (#2871, 4.5 points, apply here) for students who only attend the lectures

As usual, all lectures are public and broadcasted live so you are welcome to just show up (how to find us) or watch remotely (how to connect) without registration. Check the program as it may be updated in case of (unlikely) last minute changes.

We welcome your feedback about the quality of the webinar and the content of the lectures.

Imaging Africa workshop

Great initiative from the other side of the pond. Please forward to your imaging friends/colleagues working in African universities:

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We are pleased to announce Imaging Africa—a workshop initiative aimed at developing the microscopy knowledge and expertise of African life scientists.

Imaging Africa is an intensive, 4-day workshop + 1-day symposium focused on exposing students to a plethora of microscope technologies and impactful applications. Topics range from portable, cellphone-based microscopes to advanced super-resolution modalities. Furthermore, students will be introduced to experimental applications such as biosensors and optogenetic tools. These theoretical and practical classes will run in parallel with an in-depth quantitative image analysis course, which will provide the students with the skills necessary to reveal meaningful information from microscopy data.

With the generous support from the Gordon and Betty Moore Foundation, the Chan Zuckerberg Initiative, the Howard Hughes Medical Institute Janelia Research Campus and UNC-Chapel Hill, the Imaging Africa workshop is free of financial burden to all attending students. The expenses associated with air travel, accommodation, and food will be covered by Imaging Africa. Eligible applicants must currently be at an academic institution in the continent of Africa.

The workshop will be hosted at the University of Cape Town’s Institute of Infectious Disease and Molecular Medicine, South Africa from the 13th to the 16th of January 2020 and will be followed by a research symposium on the 17th of January 2020. Please visit www.imagingafrica.org for more information. Applications for the workshop close on the 15th of October 2019.

Please help us in making a meaningful impact on African researchers by forwarding this information to your friends and colleagues from any and all African institutions.

Sincerely,

Teng-Leong Chew, HHMI Janelia Research Campus, USA Dan Fletcher, Univ of California-Berkeley, USA Klaus Hahn, Univ of N. Carolina-Chapel Hill, USA Musa Mhlanga, Univ of Cape Town, S. Africa Kelly Rogers, Walter & Eliza Hall Institute, Australia Digby Warner, Univ of Cape Town, S. Africa

Lots of microscopy jobs around pre-Brexit Europe! :D

In the UK

I am looking for a junior scientist to develop light sheet microscopy in combination with probes to monitor cell signalling in 3D cultures, optogenetics to seed cancer causing mutations and modelling techniques to study events in early steps in oncogenesis.

The project is highly interdisciplinary but I would like to find someone who is strong on the microscopy developments.

The advert is published at the following link: https://www.jobs.cam.ac.uk/job/22329/

And a general description of the project here: https://oncolive.online/

Cheers,

Alessandro

MRC Cancer Unit, University of Cambridge Hutchison/MRC Research Centre Box 197, Biomedical Campus Cambridge, United Kingdom CB2 0XZ

https://quantitative-biology.org

In Finland

Two Research Managers in Biological and Medical Imaging for a fixed period employment at Turku Bioimaging.

Our organization

Turku Bioimaging is a research organization to employ and promote the strengths of both biological and medical imaging in the Turku region. The organization was established in 2007 and now University of Turku and Åbo Akademi University have agreed to reinforce Turku Bioimaging by strategic recruitments. The organization and its team are internationally renowned with many important national and international tasks related to coordination and promotion of imaging science. Please read more about us here: https://www.bioimaging.fi/ We are now looking for two talented persons for the positions of Research Manager. One of them will be for the field of Medical Imaging with the base location at Turku PET Centre. The other will be for the field of Biological Imaging with the base location at Turku Bioscience. https://bioscience.fi/ Positions are for a fixed period of one year, with a likely continuation for a 2-years-prolongation. After three years, the positions will be evaluated for a possible long-term continuation. Starting date is October 1, 2019 and there is a trial period of six months.

Job description

The task of the Research Manager is to support the research activities in the field of Biological/Medical Imaging within the Turku Bioimaging. The responsibilities will involve participation in the application processes and preparing applications especially for different EU funding opportunities. The tasks will also involve strengthening the roles of Turku Bioimaging in Euro-Bioimaging status as well reinforcing the position of Turku Bioimaging in Finnish roadmap for research infrastructures. The tasks will also include national coordination of the research within Biological/Medical Imaging.

What we are expecting from you

Success in the position requires a broad knowledge of techniques and concepts in Biological/Medical Imaging, including practical and theoretical understanding on how to conduct scientific research. A successful applicant should preferably also have experience in preparation, coordination, management, and reporting of research projects. As the core task for the Research Manager is related to funding, understanding of research infrastructures and how they operate (at both national and international levels) is considered important, as well as a thorough understanding of especially EU-level funding opportunities. Finally, insight into image data management is considered an advantage.

A doctoral degree in an appropriate field is required and a Docentship (adjunct professorship) in an appropriate field is considered also an advantage. The Research Manager is also required to have a good written and spoken English and readiness to travel and to represent Turku Bioimaging at national and international meetings. You also need good interpersonal skills and ability to communicate and collaborate with scientists and industrial partners from many different disciplines.

Salary and application

The salary is determined by the collective agreement system of Finnish universities. The Research Manager belongs to our research personnel and salary will be 4183 – 4500 eur/month in average.

Please write a CV and a motivation letter that describes why you are applying for the position and how you would like to develop Turku Bioimaging and bioimaging in general in Turku.

In the motivation letter, please also describe your vision of how Turku Bioimaging should be developed in terms of Biological and Medical Imaging and how the collaboration of relevant imaging scientists and centers in Finland and in Europe should be developed in the future.

Please submit your application by using our electronic application: https://www.utu.fi/en/university/come-work-with-us/open-vacancies

Application deadline is September 1st, 16:00. We will read the applications already during the application process, so please send your application at your earliest convenience. In case you need help in the application process, please don’t hesitate to contact our HR Specialist Paula Luoma paula.luoma@utu.fi.

Director, Professor John Eriksson, Turku Bioscience, tel. +358 2 215 3313, john.eriksson@bioscience.fi Director, Professor Juhani Knuuti, Turku PET Centre, tel. + 358 500 592 998, juhani.knuuti@tyks.fi

and in Switzerland

Image analysis specialist / software developer (80-100%)

Starting 1 October 2019 or as per agreement

The Biozentrum of the University of Basel is one of the leading life sciences institutes in the world. It consists of 32 groups and 500 employees that research how molecules and cells create life, spanning the scale from atom to organism. Founded in 1971, the Biozentrum has been the birthplace of many fundamental discoveries in biology and medicine, spawning several Nobel Laureates.

The Imaging Core Facility (IMCF) is a well-established technology platform at the Biozentrum offering access to high-end microscopy systems and highly sophisticated image processing IT infrastructure. The biological applications cover research areas including cellular biochemistry, cell biology, microbiology, infection biology, neurobiology and developmental biology.

The IMCF is looking for a junior image analysis specialist / software developer with a strong interest in biological applications. As an ideal candidate, you should be service-minded, proactive, and a good team player. You will be part of a team of experts designing, implementing and evaluating new software solutions for image analysis to support Biozentrum scientists in their research projects.

Your responsibilities

Typical tasks include:

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Scripting for data management tasks
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Development and implementation of image / data processing pipelines, mostly based on common bio-medical toolkits like ImageJ/Fiji, CellProfiler, QuPath, Ilastik etc.

User training and support with image analysis related topics

Many of these tasks will be done in close collaboration with our colleagues of the Research IT facility.

Your profile

We are looking for an enthusiastic person with a Master or PhD degree in Computer Science, Physics, Biology or a related field, who has proven competence in image processing and development of user-friendly software using Python, Java, Groovy and/or ImageJ-Macro. As an ideal candidate, you should be service-minded, proactive, and a good team player. We collaborate with imaging facilities and staff scientists in-house and across Switzerland, and expect you to have excellent social and networking skills and to enjoy collaborating with peers. Good communication skills in English are essential.

We offer

The Biozentrum offers a cutting-edge research infrastructure, a highly international environment, and excellent working conditions. The position is initially limited to 12 months but might be prolongated to up to 5 years. Salary and benefits according to University of Basel standards.

Application / Contact

Please apply online by 15 September 2019 with a CV, letter of motivation, and the name/address of three references: https://biped2.biozentrum.unibas.ch/apply/image-analysis-specialist

Please note that only online-applications will be accepted.

For further information, please feel free to contact Oliver Biehlmaier, PhD, Head of Imaging Core Facility (oliver.biehlmaier@unibas.ch<mailto:oliver.biehlmaier@unibas.ch>, +41 61 207 20 73)