Neubias online school of image analysis

Neubias is back with new ideas! Neubias is the Network of European Bioimage Analysts and what they burn for is to help scientists analyze their images.

Possibly inspired by the Corona time, they will start an online school for image analysis based on video tutorials and online events.

Have a look at their new page called Neubias academy where they announce several events coming up in the next few months.

A rare microscopy job in Stockholm

Dear all

If you like intravital microscopy and are looking for a job in Stockholm, check out this job ad at Stockholm University!

 

If you know anyone who is big in imaging and deserve the Lennart Nilsson Award have a look below!

Invitation to nominate candidates for the Lennart Nilsson Award 2020

Karolinska Institutet hereby invites nominations for the Lennart Nilsson Award 2020.

The Lennart Nilsson foundation was established in 1998 in order to bestow an award in recognition of the world-renowned Swedish photographer Lennart Nilsson and his extraordinary body of work. Its main aim is to promote education, training and research within the medical, biological and engineering sciences through the use of images.

This is achieved through the Lennart Nilsson Award, an international award bestowed annually upon an individual in recognition of outstanding contributions within the realm of scientific photography.

The nominees should fulfil the following criteria:

  • Work in the spirit of Lennart Nilsson
  • Make the invisible visible
  • Reveal sciences to the world in beautiful, unique and powerful ways
  • Visualize a scientific breakthrough
  • Image reality in a surprising way

You are invited to nominate candidates to the Lennart Nilsson Award. Candidates should be active mainly in the Life Sciences and use pictorial representation as an explanatory medium. Users of animation technology are also eligible. The enclosed nomination form should be filled out and sent in together with the candidate’s CV, bibliography, articles, technical descriptions and pictorial material. Up to three letters with references and comments from experts may be included. Please attach the material as one PDF-file if possible and send to fonder@ki.se no later than Tuesday April 28, 2020. If you need to submit a larger file, you can send an e-mail to us for assistance.

The awarded amount is SEK 100 000 and the prize ceremony will take place in connection with the installation ceremony for new professors at Karolinska Institutet, Stockholm, Sweden October 15th.

More information about the Award can be found on  http://ki.se/en/about/the-lennart-nilsson-award

For further questions please contact fonder@ki.se

 

 

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.

Microscopy job in Manchester

Senior Experimental Officer (Bioimaging / Image Analysis) The University of Manchester, UK

The University of Manchester Bioimaging Core Facility is recruiting an image processing/analysis Senior Experimental Officer. This position is initially for 2 years, but with a view to becoming a permanent position. Manchester is a great place to live and work and you’ll be part of a team supporting over 20 microscope systems and 200 PIs. We run a mix of commercial, open source and bespoke software and the successful candidate would be responsible for developing, applying and teaching these tools to the Facility users. You don’t need to be from an academic background, we’d be very keen to recruit someone currently working within the commercial side of image analysis and a PhD is not essential – we’re looking for the right person not the right qualifications.

Due to the demand for advanced image processing and data analysis, a new position has been created to support the users of the Bioimaging Facility in the Faculty of Biology, Medicine and Health.

You will work as part of the Bioimaging team, led by Dr Peter March, but you will be responsible for developing the image processing capabilities of the Facility. Combining both commercial packages and your own bespoke scripted solutions you will provide analysis pipelines to support users who have acquired large multi-dimensional datasets using the Bioimaging Facility microscopes. You will have multiple projects to manage simultaneously and so excellent project management skills are also required.

You will have completed a PhD in science, mathematics, computer science or a relevant discipline, or equivalent experience. A knowledge of cell biology is not essential, but you must have proven experience in developing analysis pipelines and the ability to write custom scripts. Excellent communication and interpersonal skills are also required.

As an equal opportunities employer we welcome applicants from all sections of the community regardless of gender, ethnicity, disability, sexual orientation and transgender status.  All appointments are made on merit.

Please note that we are unable to respond to enquiries, accept CVs or applications from Recruitment Agencies.

Enquiries about the vacancy, shortlisting and interviews:

Name: Dr Peter March

Email: P.March@amcnhester.ac.uk Tel: 0044 161 275 1571 or 0044 7747 118 447

General enquiries:

Email: hrservices@manchester.ac.uk Tel: 0161 275 4499

Technical support:

Email: universityofmanchester@helpmeapply.co.uk Tel: 0161 850 2004

This vacancy will close for applications at midnight on the closing date.

Closing date: 30/01/2020

Salary: £41,526 to £51,034 per annum according to relevant experience.

Employment type: Fixed Term

Department: Biology, Medicine & Health

Hours per week: Full time

Contract Duration: From January 2020 until 31 December 2022 Job reference: BM&H-14959