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/
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
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! 🙂
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.
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/
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!
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.
