The Live Cell Imaging facility
@ Karolinska Institutet, Sweden
Here are a few image analysis tools (constructs for FRET, software…) that might be useful to you.
http://www.hahnlab.com/tools/index.html
https://www.utsouthwestern.edu/labs/danuser/software/
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:
Wow! What a year! 😃
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.
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! 😊
The microscopy field is moving away from blue dyes. This is because red light, used to excited far red and deep red fluorophores, is less damaging to live cells than near UV light which is used to excite blue fluorophores.
On top of that, red light penetrates deeper into thick samples.
So as the trend in microscopy is to move to thicker samples and use more live samples, far red and deep red fluorophores are becoming more attractive.
Here is an article describing 3 new fluorescent protein in the far red to deep red range. One can excite them with 640 nm or a 685 nm lasers or LEDs.
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! 😀
Anyone feeling like working in Singapore? Here is your chance! 😁
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!
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.
To image a thick sample, it is crucial to match the refraction index of the sample with that of the immersion medium between the sample and the objective. Typically, life samples are in an aqueous solution like culture medium which has a refraction index of 1.33. Unfortunately organoids often have a higher refraction index closer to 1.44 therefore as one images deeper into the organoids, light scatters due to the refraction index mismatch and the images become blurry.
This paper presents a product that has a high RI and is compatible with cell culture. Good to keep in mind for those who image organoids over time.
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! 😀
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:
Great initiative from the other side of the pond. Please forward to your imaging friends/colleagues working in African universities:
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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
