Supplies of Zell Kontakt products

Zell Kontakt is a German company making fantastic glass bottom dishes and plate. Check out why the LCI facility likes their products (absolutely no commercial interests!).

Great products but crap communication skills! Either their website is down or they do not answer the phone and emails and anyway if they do, make sure you have a German colleague around because no one speaks English.

Now we have found a way around the problem: MoBiTec sells Zell Kontakt products. πŸ™‚

Free genetic and image analysis tools

Here are a few image analysis tools (constructs for FRET, software…) that might be useful to you.

  • Construct for fluorescence biosensors and optogenetic tools
  • Free Image analysis software

http://www.hahnlab.com/tools/index.html

  • Free Image analysis software

https://www.utsouthwestern.edu/labs/danuser/software/

  • Free Image analysis software

http://cismm.web.unc.edu/

Party time at the LCI! :D

On the 10th of October, the Live Cell Imaging facility will have an open house and a little party to celebrate loads of great stuff:

  • The LCI turned 10 years old this year! 😊
  • We got a wonderful light sheet system earlier this year. It is high time to give it a name and splash it with a bit of champagne!
  • Gisele Miranda from Scilife/BII has joined the LCI team to help our users with image analysis
  • We got a great server/analysis capacity set up by the KI IT department

Wow! What a year! πŸ˜ƒ

Please come and celebrate with us! If you do not know what our microscopy facility has to offer, it is time to be curious and pay us a visit.

  • Open house: drop in between 9:00-11:00
  • Baptising of the light sheet system and celebration of Gisele and our shiny new server: at 11:00

All this will happen on the 10th of October (next Thursday) at the LCI facility, on the 7th floor of Neo at KI Flemingsberg. Here you can see how to find us.

Please help us spread the news! 😊

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! πŸ˜€

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

Neubias school for image analysis 2020

Neubias is a European effort to get biologists to analyse their images by locking them in a room with some image analysis experts. If you get accepted to the Neubias school, you get to learn image analysis on your own data and you get expert help to build your pipeline!

The next Neubias school will be in the beautiful city of Bordeaux in February 2020. Apply soon not to be disappointed! πŸ™‚

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 πŸ˜‰

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

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).

Call4Help: The image analysis help you have always dreamt of, totally for free!!! ???

After the success of the previous Call4Help session in February, BII (BioImage Informatics, the great image analysis at SciLife Uppsala) and your favorite microscopy facility (we hope) will run a new Call4Help next Tuesday 2nd of April.

Anyone who is stuck with image analysis and wishes for quick help can apply.

These are 100% online sessions (we β€˜meet’ in a Zoom chat room) where you submit your images and a little explanation text in advance and you get suggestions for 30 min and an analysis pipeline all done for you (Fiji, CellProfiler, Ilastik, QuPath, KNIME)!

If you are interested, please apply as soon as possible (sorry for the late announcement).

Here is how to apply: https://www.scilifelab.se/facilities/bioimage-informatics/

Are there brighter versions of GFP or RFP out there?

Have you ever heard about Superfolded GFP? It is 50% brighter than GFP! And mScarlet is almost 6 times brighter than mRFP! How do I know? I look at this fantastic database called FPBase.

You can see which fluorescent protein is monomeric, sort them by excitation and emission or find which bleaches least or maturates fastest! Great tool! πŸ™‚

Fluorophores are constantly being developed. If you make a new plasmid, make sure you check that the one your lab has been using for trillions of years is the very best one!