I am wowed at the images published recently in BioArxiv in the Zero-shot deconvolution networks paper. It will be interesting to see the peer-reviewed paper.
I would be interested in visualizing the amount of errors made by the network. A simple way to do it is to acquire a short time lapse (eg 10 images) of a fixed sample, run it through the network and see which structures are stably identified and which change from frame to frame. 🙂
Microscopy course: improve your imaging skills – from sample preparation to image analysis
Starting from next week, the Live Cell Imaging core facility at KI will run its yearly microscopy course.
All the course lectures will be broadcasted live on Zoom, free of charge and there is no need to register. On this page, you can find the course schedule (public activities are in blue) and the Zoom link to join. Scroll down to read the student testimonies! 😊
30 Jan – 17 Feb 2023
The aim for this course is to improve the microscopy skills of students and researchers who have already used a microscope to acquire digital images of fluorescent samples but feel that more knowledge could help them.
The course covers the following topics:
- Optics, image formation
- Fluorescence, fluorophores
- Anatomy of a microscope
- Objectives and refraction index
- Cameras and detectors
- Noise and background, Bit depth and saturation
- Multichannel imaging and spectral unmixing
- Resolution and contrast
- Sample preparation, Immunostaining
- Nyquist sampling
- Confocal and wide field settings
- Speed, High throughput/content
- Volume imaging, deconvolution
- Clearing and expansion
- Live cell imaging
- AI, Super Resolution microscopy
- Data handling, OMERO.figure
Hope you enjoy the Live Cell Imaging core facility microscopy course! 😃
It is time to enroll to the yearly light microscopy course run by the Live Cell imaging core facility (30 Jan – 17 Feb 2023): ‘Microscopy: improve your imaging skills – from sample preparation to image analysis’ (6 credits).
- Check the course schedule to see the course content and testimonies from alumni
- If interested, you can enrol as a student. Please read carefully the eligibility criteria and note that the last registration date is the 15th of November.
Additionally, all the lectures (in blue on the schedule) will be publicly broadcasted live on Zoom and accessible to anyone without registration. Even if you do not want to enrol as a student, you can have a look at the and listen to any lecture that triggers your interest. There is no need to register. The schedule and zoom link are on the course page.
The purpose of this course is to enable PhD students and researchers who have already and recently used a microscope to acquire images of fluorescent samples, to improve their microscopy skills.
The course is NOT aimed at training people to use the LCI facility microscopes. The focus is instead on providing the students with enough theoretical and practical knowledge about their OWN sample and their OWN microscope, to enable them to:
1) prepare their sample and formulate their scientific question in a way that is suitable for data extraction from fluorescence images
2) properly use the hardware available in their lab/facility and 3) fully understand each parameter they need to set in the software in their lab/facility.
The aim is to provide the course students with the tools to acquire on ANY wide field, confocal or light sheet microscope, images of their samples that reliably answer their scientific question.
Please help us spread the word. 😃
Light-Seq is a new pretty cool technique for highly multiplexed sequencing of RNA in tissue sections using light. This technique is highly sensitive, highly spatially resolved and because it does not destroy the tissue, it can be combined with protein labelling (genetic or by immunolabelling).
On one of our single-point confocal/spinning disk/widefield system at the LCI facility, we have a device called Primo (DMD + UV laser) which can be used to run this technique! 🙂
Let us know if you would like to set up LightSeq at the LCI core facility!
On the 22nd of September at 10, you get a chance to see and try the latest light sheet on the market: the Nikon Mizar TILT.
- Easy to use stage top light sheet with only 1 objective
- Imaging of cell monolayer, cells in gels, organoids in gels, small organisms…
- Samples in glass bottom multiwell chamber slides
- Stage top incubator for live sample imaging
- Advantage of using the TILT light sheet
- low phototoxicity and bleaching even with high resolution objective
- excellent temporal and spatial resolution for live samples
- See here for more info.
This demo is only for a limited time (10 days) and in person only. Please let us know if you want to join the demo and if you want to try your own sample.
9th of September, 10-12am: Live/zoom demo of the latest microscope acquired by the LCI facility: Crest spinning disk with DeepSIM (new Orion)
- Ti2 microscope
- Crest spinning disk (identical to the one on Tweety but with slightly different wavelengths)
- DeepSIM: SIM is a fast super-resolution technique which is gentle for the sample (less bleaching, less photodamage for live samples) and offers double the resolution of a confocal microscope (down to 120nm resolution), even thick in samples. It is flexible and can be used with any objectives, even low magnification air objectives.
- No specific sample preparation requirements
- More information here
For the best experience, join the demo in person at the LCI facility (please apply by replying to this email) but if you cannot make it, you can also listen on Zoom.
The system has been purchased by the LCI so it is here to stay! 🙂
Please let us know if you want to join the demo in person and mention if you would like to try imaging your own sample with DeepSIM.
mCherry is a very popular red fluorescent protein. However it has several disadvantages:
- It is shifted towards far red (ex peak 585 nm) so it often is not imaged optimally with the illumination sources and filters commonly available.
- It bleaches fast
mCherry has now been evolved into mCherry-XL with several improvements:
- This variant is shifted back towards green (ex peak 560 nm) therefore being very well excited with popular 561nm lasers.
- It is 3 times brighter than mCherry
- There is also a clear improvement in the lifetime for FLIM
- Together the 2 points above means that less excitation power is required so it should help with the bleaching problem
Here is the paper. Therefore you should consider mCherry-XL for your future tagging with red fluorescence proteins.
Nikon Europe recruits an image analyst in Leiden.
See here if this is the dream job for you. 🙂
The BioImage Informatics facility at Scilife organizes a new presentation on free and open-source tools: TissUUmaps, a browser-based tool for GPU-accelerated visualization and interactive exploration of millions of datapoints overlaying tissue samples.
Users can visualize markers and regions, explore spatial statistics and quantitative analyses of tissue morphology, and assess the quality of decoding in situ transcriptomics data. TissUUmaps provides instant multi-resolution image viewing, can be customized, shared, and also integrated in Jupyter Notebooks. TissUUmaps was created in collaboration between BIIF and the Wählby lab. You can read more about it and test the software on its web page: https://tissuumaps.github.io/
During the seminar, we will go through basic usage of TissUUmaps: installation, loading images, markers and regions, change visualization settings, and how to load / save / share projects. The webinar will be given by Christophe Avenel and will take place on March 3rd, 09:00-10:00 (instead of our normal Call4Help session). There will be time for questions and discussion, so we hope this event to be very interactive. Please register here.
Nordic superresolution microscopy facility staff/researchers: STED
March 15th and 16th at 9-12 am. CONTACT: Hans Blom (email@example.com)
Mar 15, 2022 9:00am
- 9:00-9:45am – BNMI info / STED intro [Hans Blom & Daniel Smeets (Leica)]
- 9:45-10:15am – STED sample prepping [Ulf Schwarz et al. (Leica)]
- 10:30-11:00am – Input from a Nordic STED facility [Jonathan R. Brewer (DaMBIC)]
- 11:00-11:45am – STED demos [Luis Alvarez/Ulf Schwarz et al. (Leica)]
- 11:45-12:00am – Extra discussion time
Mar 16, 2022 9:00am
- 9:00-9:45am – Live-cell STED [Giovanna Coceano (KTH Stockholm)]
- 9:45-10:15am – Remote STED [Marko Lampe (ALMF/EMBL)]
- 10:30-11:00am – STED-FCS [Erdinc Sezgin (KI Stockholm)]
- 11:00-11:45am – Advanced STED demos [Luis Alvarez/Ulf Schwarz et al. (Leica)]
- 11:45-12:00am – Extra discussion time