Great help with image analysis: application deadline tomorrow!

Tomorrow 30th of May is the last day to apply to the Neubias (Network of Bioimage Analysts) image analysis school in Porto in October!

If you have any scary image analysis problem sitting under your bed at night, Neubias is for you 😉

Neubias is a great opportunity to get started/go deeper with image analysis and get your analysis pipeline written by experts.

Super-Resolution spinning disk demo at the LCI!

Dear microscope freaks

How would you like to run some gentle live sample imaging with a 60x objective with:

  • an xy resolution of 120 nm without software tricks (or even better after deconvolution),
  • the great contrast of a true confocal,
  • 82 frames per second,
  • or decide to bypass everything, go widefield and image at 100 frames per second with a super large field of view (220×220 um)?

Sounds good to me! 🙂

For the next 2 weeks you can do that with the new toy on demo at the LCI facility!

The beast is a new sort of spinning disk confocal and is called SoRa (Super-Resolution Optical Reassignment). It is a collaboration between Nikon and Yokogawa.

We even have 2 cameras to compare (Prime95B and BSI from Photometrics).

Oliver Garner from Bergman Labora will give a short online presentation of how SoRa works on Monday (29th) at 13:00. The presentation is done remotely and broadcasted live. You can join the audience from the comfort of your office chair by following the instructions here (please try beforehand to make sure all works).

Interested in trying it? Please contact us.

A dream!!

Imaris workshop at the LCI: rescheduled to the 22nd of May :)

Imaris is a great image analysis software that is available to all the members of the Live Cell Imaging facility.

It is as easy to analyse 2D and 3D image files with Imaris. The software also allows you to make great multidimensional plots to present your data.

One can count objects inside objects (example number of vesicles per cell), measure shortest distances from one type of object to another (example distance from vesicles to the cell membrane), track cells even when they divide, trace neurons or blood vessels… all this in 3D, time, several colours.

On the 22nd of May, the LCI will host an Imaris workshop.

The morning seminar (held in Neo/DNA room) from 10-12 will be broadcasted for those who cannot join. Please follow the instructions on our website to follow the webinar.

In the afternoon, we will analyse the data of our users. Submit your images to DONTCHEVA Guergana (g.dontcheva(at)bitplane.com).

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?

Step1:

Prepare a presentation – use this template for your presentation:

Step2:

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

Participants

Petter Ranefall

Kevin Smith

Anna Klemm

Sylvie Le Guyader

Call4Help format

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

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! 🙂

 

More about RNA labeling

Yet another chance to try RNA labelling: The FENO facility, here in Flemingsberg, has purchased a machine to multiplex RNA scope. They will present it on the 16th of October. 🙂

Here is the announcement.

Clearing and expansion microscopy course at Scilife in September!

Expansion microscopy and clearing are fantastic tools for anyone who images thick (> 1 cell diameter) fixed samples. We are now lucky to have access to state of the art talks and hands-on workshops at Scilife in September. Register early not to be disappointed!

Please apply to Hans (first day) and David (second day) directly!

Neubias workshop for image analysis at the heart of Scotland!

Here is where to register for the next Neubias, the European Image Analysis school! Learn how to build your own image analysis pipeline with expert help! 🙂

Only a few days left to register!

Learn about Expansion microscopy

Next wednesday morning, David Unnersjö-Jess from KTH/Scilife will give a talk at the Live cell imaging facility (9:30, DNA seminar room), about a new and exciting aspect of microscopy: Expansion microscopy.

This is a technique where one ‘blows up’ the sample while keeping all proteins in place and at the same relative distance from each other. The sample is simply ‘inflated’. One can then take images of it with a normal microscope but the resulting image give a much higher resolution than normal microscopy.

After the seminar, David will have an open discussion with anyone who would like to try the technique.