Rare: 2 permanent microscopy jobs in Stockholm!

Hi there

I don’t get to post this type of announcements on a daily basis! 2 microscopists are required at the Cell Profiling facility at SciLife!

See here for details.

Lots of Image analysis courses in Uppsala! :)

Biovis is the image facility at Uppsala University, just a stone-throw away from us. Every year, they run several Image analysis courses, from short introductions to full blown courses.

Have a look here!

CUBIC seminar tomorrow at Scilife

Do not miss the seminar tomorrow morning at Scilife: the inventor of the CUBIC technique, Etsuo Susaki, will present his technique which can clear fatty and dense tissues.

Click here to know where and when.

Antibody-based technologies at SciLife

Apply to this course at SciLife and learn about Antibody-based technologies on the 25th of March.

Image Analysis Call4help on 14th of feb!

The image analysis help you have always dreamt of, totally for free!!! 😱😱😱

Deadline 6th of feb!

First SciLifeLab BioImage Informatics call4help zoom session

On the 14th February 2019, 10:00 – 12:00 the SciLifeLab BioImage Informatics Facility is organizing an online support session on BioImage Analysis (“call4help” session).

How does it work?

Each selected participant gets a 15 min slot. You have 5 min to present your problem. It is mainly about showing the scientific context, representative input images, describing desired output measurements, and giving a brief statement about what was done before. The remaining 10 min we will brainstorm together on the possible solution(s), discuss tools, techniques, etc.

The Bioimage Informatics Facility can provide further support, if needed. We are happy to announce that Sylvie Le Guyader, Live Cell Imaging Facility, KI, Huddinge, is joining the session as microscopy expert.

How can I participate?


Prepare a presentation – use this template for your presentation:


a) Upload your presentation to this google drive:

b) AND send an e-mail to anna.klemm@it.uu.se until 6th February 2019.

Step 3:

Join this zoom-session.

If your problem is selected for presentation, you will get a time-slot of 15 minutes within the session (14th February 2019, 10:00 – 12:00). If not, you are welcome to join the discussion anyway!

What are the Deadlines

Submission of a problem: until 6th February 2019

Notification about participation: 8th February 2019

Session: 14th February 2019, 10:00 – 12:00


Petter Ranefall

Kevin Smith

Anna Klemm

Sylvie Le Guyader

Call4Help format

The call4help format was initially developed by ScopeM, ETH Zürich.

Matching the Refraction index of the sample with the objective

Together with the coverslip and the immersion medium (oil, water, glycerol or air), the sample mounting medium is part of the design of a microscopy objective. Matching the refraction index of the sample to the one recommended by the manufacturer of the objective will make the sample transparent for the objective, drastically improving fluorescence microscopy in samples thicker than a couple of um (i.e. anything except fluorescent beads!).

Not matching the refraction indices is equivalent to watching something through a wet window… Far from optimal! :-/

The refraction index recommended by the manufacturer is the same as the RI of the immersion medium: 1.52 for an oil immersion objective, 1.47 for a glycerol objective, 1.33 for a water objective, 1 for an air objective.

This article compares 7 mounting media and their effect on the refraction index of brain samples. CFM3 seems to be a cool mounting medium. The company that produces it has partially paid for the study but it sounds worth a try anyway!

In the same vein, this article presents a non-toxic way to change the refraction index of cell culture medium (not the sample) to improve imaging of live samples. Sounds pretty promising to grow live organoids which quickly become opaque.

If you try any of these 2 chemicals, please leave a comment to let us know how it went! 🙂

Image analysis primer or more!

Registrations are open now for 2 fantastic ways to reach the stars with your image analysis:

Ready? Get set! Go! 🙂

LCI microscopy course vintage 2019! :)

The Live Cell Imaging facility is back with its intensive microscopy course! In 2018 we moved to a new building so there was no course but we will strike again in Jan-Feb 2019!!You will definitely learn tons at our course. Have a look at the program and judge for yourself.

As usual we run 2 courses in parallel:

#2870, 6 points, is the full course with all lectures, workshops, demos… This will run 22/jan-08 feb, 3 days/week 9:00-17:15.

#2871, 4.5 points, is the same minus some workshops and demos. This course will run at the same dates but 10:00-15:00.

The rest of the time is used for home assignments.

All lectures are open to the public without any registration so tell your colleagues!

Course applications are open from today and until the 15th of November. The full course (2870) has only 16 spots available so just go for it NOW! 🙂