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! 😀

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.

Seminar on how to directly label your primary antibodies: Skip the secondary, part 3!

The LCI will host a seminar about GlyCLICK, a new way to directly label primary antibodies and stop using secondaries: 6th of November at 13:00 in the Lipid seminar room in Neo, KI Flemingsberg. The seminar will be broadcasted live. Here is how to find us and here how to follow the seminar online.

Everyone agrees that it would be great to be able to label our samples without using secondary antibodies.

  • less animals killed
  • shorter and cheaper protocols
  • no problem with isotype cross-reaction
  • no problem with secondary species when using many antibodies at once

There are many kits to label primary antibodies directly with fluorophores. The main disadvantage compared to primary/secondary stainings is that direct labels are often weaker because the final primary/fluorophore ratio is too low. Using an amplification method like TSA (Tyramide Signal Amplification) leads to a loss of resolution.

Over the years users at the LCI have tried this kit, this kit and this one. They gave mixed results depending on the antibody but we keep looking! Come to the LCI seminar about a new direct labelling technique that uses Click chemistry.

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.

EMBL microscopy event in Göteborg

Nice speaker line up at this 1 day event on the 18th of october.

Organized by Astra Zeneca, EMBL and several Swedish universities, this is a good mingling event for microscopists! 😀

Crest V3 spinning disk confocal demo

Tomorrow (17 sept) we will enjoy a seminar and a live demo about the Crest V3 spinning disk confocal which is being set up at our facility as I write! 😀

Very cool confocal!

  • enormous field of view (32 mm diameter)
  • fully confocal
  • can image at 100 frames per sec
  • spits out Nyquist resolution with the 60x objective!

You can come to the seminar (at 10 in the Gene seminar room at the LCI facility) or listen to it remotely (see here how to follow the LCI webinars).

You can even book a private demo to image your own samples.

How to identify cells and nuclei in an image?

NucleAlzer is a great new deep learning tool to identify roundish objects like nuclei and cells in fluorescent or bright field images.

To test if the tool works for you before you download it, you can simply upload one of your images and check the result. Easy! 😀

Call4Help: fast-track help with your image analysis project!

BII (BioImage Informatics, the great image analysis at SciLife Uppsala) and the LCI facility will run a new Call4Help on the 4th of September.

Anyone who is stuck with image analysis and wishes for quick help to build a pipeline should apply. You don’t have to acquire the images at the LCI. Anyone can apply.

How does it work? You first upload your images and a little explanation text. A few days later, we all meet virtually in a Zoom chatroom for a quick (30 min-1 h) online session. You get comments, suggestions and help with building a Fiji or CellProfiler analysis pipeline tailor-made for your images.

If you are interested, click on the link below to apply:

BioImage Informatics

Imaging Africa workshop

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

—————————————————–

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

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