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).
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 ‘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/
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! 🙂
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!
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.
On Thursday (15th of March), Teng-Leong Chew, director of the Advanced Imaging Center at the Janelia Research Center (Virginia, USA), will come to Stockholm and present what his facility can potentially do for you.
The AIC offers a crazy service where visiting scientists can use the super resolution systems they develop there with the help of their experts. This service is free of charge, including accommodation.
This can allow you to quickly run a project involving STED, PALM/STORM, SIM, adaptive optics or super resolution lattice light sheet microscopy.
Together with Leong’s presentation of his facility, there will be a few seminars by the Live Cell Imaging facility as well as several parts of the Advanced Light Microscopy facility at Scilife.
This is a great opportunity to catch up with what is available to you here and in the US. Hope to see you there! 🙂
One more cute stage insert for the LCI facility, thanks to Peter Arfert, the KTH workshop wizard and his 3D printing machine! 🙂
This course about light microscopy is made of videos only! It is very complete, very interesting and very well done!
Point Spread Function? Fourier transform? Image formation? Resolution? Everything about light microscopy you wish you had learned earlier! 🙂
Do your bit as a microscopy geek and download a great app called Resolution!
You can enter your objective of choice (magnification and NA) and get for the wavelength of your choice loads of useful information like the resolution in xy and z the optional sampling step…
But if you REALLY want to enter thegeek club, you must also get the Fourier Filter app! Hours of geeking fun ahead of you! 😉
Did you know about the BioImage Informatics Facility at Scilife? This is a great facility for image analysis. You can get 20h of expert help for free? Contact Petter Ranefall to get help with your analysis!
Are you desperately looking for a small replacement part for some machine? Or as we did, a custom-made stage insert for our microscopes to accommodate 4 slides?
KTH has a very good 3D printing machine and Peter Arfert peter.arfert-at-sth.kth.se will work it all out in a blink!