Cool technique – The Live Cell Imaging facility

Direct label of primary antibodies with the FlexAble kit

Some of our users have tested the ProteinTech FlexAble kit to directly label primary antibody and they are very happy so we thought we should share! 🙂

It only takes 10min to label the primary. It saves time for the sample staining procedure and it saves cute animals when one stops ordering secondary antibodies! 🙂 In the hand of our users, the images were as bright or brighter than the same labelling with primary + secondary.

And you can ask for a free sample to test! :):):)

Gisele is hiring!

At the LCI, we have a long standing collaboration with Gisele Miranda, a great and kind image analyst affiliated to BIIF. Gisele is now starting her own image analysis lab! She is currently hiring 2 PhD students so if you know anyone interested, please spread the word. Here is what Gisele says:

I am excited to share that I have recently started my own research group as a SciLifeLab Fellow at KTH Royal Institute of Technology and the Science for Life Laboratory in Stockholm, Sweden. My group will focus on developing and applying cutting-edge Machine Learning techniques to deepen our understanding of cellular behavior and interactions. With a strong emphasis on generative AI, we aim to explore diverse data types, such as microscopy images and omics data, to simulate and predict biological behavior. Our work will focus on mapping complex relationships between single-cell and spatial features, driving new insights into the underlying architecture of cellular networks.

As part of building my group, I currently have two open PhD positions. I would deeply appreciate your help in spreading the word about these opportunities to potential candidates who are interested in working at the intersection of AI and biology.

https://www.kth.se/lediga-jobb/751352?l=en

https://www.kth.se/lediga-jobb/758900?l=en

Thank you for your support, and I look forward to staying connected as my group takes shape!

Best regards,
Gisele

BIIF is hiring!

The BioImage Informatics facility at Scilife is hiring 2 image analysts! Here are the ads:

Open Positions @BIIF

A permanent bioinformatician position (6-month trial period) located at Uppsala University, Department of Computer Science.
Research Software Engineer position located at our KTH site in Stockholm Solna. This is a 1-year position, but there is a possibility to extend it to a permanent position after.

Please contact BIIF directly if you have any question.

Open house at the LCI facility on 24th of September

Dear microscopy enthusiasts,

The Live Cell Imaging core facility is happy to invite you to a microscopy event on Tuesday, 24th of September.

You will have the opportunity to see Nikon ECLIPSE Ji Smart microscope in action!!!! A fast and easy to work with benchtop microscope with many ready to run experimental assays, AI powered automated imaging and instant image analysis!!!!

We are also showing the power of our CrEST V3DeepSIM super-resolution microscope, that offers double the resolution of a confocal microscope (down to aprox. 100 nm resolution in xy; 300 nm in z), even in thick samples. Flexible and can be used with any objectives, even low magnification air objectives!!!!

Do you want to image large, cleared samples? No problem, come to our demo and see our fast imaging light sheet microscope from M Squared in action!

Program

9:30-12.15 Open house: Come and ask questions about microscopes at our facility! Drop in.

9.30-10.00 Public demonstration of CrEST V3 spinning disk microscope

10.00-10.45 Public demonstration of the Nikon ECLIPSE Ji Smart Imaging microscope

10.45-11.00 Coffee

11.00-11.45 Public demonstration of the CrEST V3 DeepSIM super-resolution microscope

11.45- 12.15 Public demonstration of the Light sheet microscope from M Squared

13.00- 17.00 Private demonstration (bring your own sample) on ECLIPSE Ji and CrEST V3 DeepSIM

Registration is mandatory for private demonstration. Register by sending an email to gabriela.imreh@ki.se latest on 23^rd of Sept. Mention which instrument you would like to have the private demonstration on.

Venue: Flemingsberg Campus Neo, Karolinska Institute, Blickagången 16, Floor 7.

Please call us so we can let you in. (Gabriela Imreh 0707480761; Sylvie Le Guyader: 0737335008; Jianjang Hu: 0729087375)

Please share this event with friends and colleagues who may also be interested in attending this event.

The LCI core facility is now a member of Eurobioimaging!

Good news! The LCI facility is now part of the Swedish Eurobioimaging node! 🙂

This means that you can apply for funds to come and get trained, do some job shadowing or image at the LCI core facility!

The Swedish Eurobioimaging node is even partner in special European funding programs for Agroecology, and Cancer research.

We are looking forward to welcoming you to our facility! 🙂

The LCI open microscopy course starts on Monday! :)

Dear all

It is my pleasure to invite you to follow the LCI facility microscopy course Microscopy: improve your imaging skills – from sample preparation to image analysis.

The course starts next Monday (29 Jan) and runs until the 16^th of February.

As usual, all the course lectures are broadcasted live on Zoom. It is free of charge and you do not need to register.

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.

Here is a selection of what we will talk about:

Optics and image formation,
Anatomy of a microscope
Objectives and refraction index
Cameras and detectors, Noise and background, Bit depth and saturation
Sample preparation, Immunostaining, Clearing and expansion
Resolution and contrast, Nyquist sampling, Microscope settings
Data handling, OMERO.figure, Requirements for image analysis, Colocalization
Image processing and analysis

Check our course webpage to see the course schedule (Broadcasted activities are in blue) and the Zoom link. Scroll down to read the kind testimonies of our dear students! 🙂

Here is the course syllabus.

For those who are on a far away time zome, we record all the live lectures and post them every evening on the LCI facility YouTube channel! 🙂

We hope that you will enjoy the LCI facility microscopy course!

Kindly forward to anyone who might be interested.

The LCI team

Spatial transcriptomics in Flemingsberg!

Spatial transcriptomics techniques are booming! It is now possible to identify where RNAs are located within a tissue! At the LCI facility, we routinely image samples labelled with RNAscope. If you use RNAscope, you might be interested in this workshop where you will learn how to label thick samples with RNAscope, and this symposium about automated RNAscope.

Additionally, we can now offer the 10x Genomics Visium technology on the South Campus, as a collaboration between 4 core facilities in Flemingsberg: LCI, FENO, SICOF and BEA core facilities!

Here is the workflow:

We discuss your project and advise you for the preparation of your sample.
You cut your sample and optimize the antibody or H/E staining yourself, under the guidance if the LCI staff to best preserve the RNAs.
You image your tissue sections at the LCI facility.
You transfer your section to SICOF who tags the RNAs and amplifies the library, using the 10x Genomics Visium technology.
The library goes to BEA for sequencing.

Section size: max 6.5×6.5 mm or max 11×11 mm
Human or mouse
Paraffin-embedded or fresh-frozen
Labelled with H/E or fluorescent antibodies

Come and talk to us about your Spatial Transcriptomics project!

Nordic Microscopy Symposium – 3rd-5th October

We are delighted to invite you to the Nordic microscopy symposium at the Live Cell Imaging core facility, Nikon Centre of Excellence at Karolinska Institutet, organised by BergmanLabora, Ramcon Denmark and Inter Instrument AS.

The symposium will highlight the great research done in the Nordics where microscopy is a key tool.
New exciting equipment from Nikon will be showcased including the AX/NSPARC super-resolution point confocal and the CrEST DeepSIM super-resolution spinning disk confocal.
We will also be launching the new Nikon Eclipse Ji benchtop assay instrument and demo the simpler CrEST Cicero spinning disk confocal.
The capability of these systems will be demonstrated during public sessions (3^rd of October) and in private sessions (on 4^th and 5^th October) where you are welcome to bring your own samples.

Venue: Neo, Flemingsberg Campus, Karolinska Institute: Erna Möller Lecture hall (Symposium), Live Cell Imaging (LCI) core facility (Demos)

3rd October

- 1000-1145 Public demo: Nikon AX R NSPARC super-resolution point-scanning confocal, CrEST X-Light V3 super-resolution spinning disk confocal, CrEST Cicero compact spinning disk
- 1000-1145 Open house at the Live Cell Imaging core facility (Drop in. Contact Sylvie Le Guyader)
- 1200-1300 Lunch (requires pre-registration)
- 1300-1305 Welcome
- 1305-1345 Zuzana Kadlecova (Cambridge Institute for Medical Research – UK): Lights! Camera! Uptake! Zooming in on Endocytosis with Quantitative TIRF-SIM Analysis.
- 1345-1410 Nicoline Dorothea Daugaard (Dept. Biochemistry and Molecular Biology, SDU – Denmark): Tracking T cells and their interactions with cancer cells in 3D using NIS-Elements General Analysis (GA3)
- 1410-1440 LCI short talks:
  - Chiara Annunziata (Karolinska Institute – Sweden): A pipeline for the multiparametric assessment of the anti ageing effects of candidate molecules
  - Andrea Coschiera (Karolinska Institute – Sweden): Primary cilia promote the differentiation of human neurons through the WNT signaling pathway
  - Natalie Geyer (Karolinska Institute – Sweden): Multiplex RNA in situ hybridisation for liver parenchyma characterization in a metastatic context
- 1440-1500 Coffee
- 1500-1525 Technical talk (Nikon): Microscopy Simplified, Nordic Launch of Nikon’s new ECLIPSE Ji
- 1525-1540 Staffan Strömblad (Karolinska Institute – Sweden): Multi-site assessment of reproducibility in high-content cell migration imaging data
- 1540-1605 Pieta Mattila (University of Turku – Finland): Advanced imaging methods to visualize lymphocyte activation

4th and 5th October

- 0830-1700 Private demos (bring your sample) Nikon AX R NSPARC super-resolution point-scanning confocal, CrEST X-Light V3 super-resolution spinning disk confocal, CrEST Cicero compact spinning disk
- 0830-1700 Open house at the Live Cell Imaging core facility (Drop in. Contact Sylvie Le Guyader)

Registration is mandatory and can be done via the following site: Nordic Microscopy Symposium – BergmanLabora.

Please share this event with friends and colleagues who may also be interested in attending.

Clearing and expansion microscopy symposium and workshop sept 12-14

Two really nice symposia/workshop on clearing and expansion microscopy next week!

At the Wenner-Gren Center in Stockholm SEPT 12th (9 am – 2 pm), experts in the field present developments and applications. https://bnmi.eu/symposium-on-clearing-expansion-microscopy-in-stockholm-solna-sweden-september-12-14-2022/
At SciLifeLab in Solna SEPT 13-14th, experts from academia and industry present applications. https://bnmi.eu/symposium-on-clearing-expansion-microscopy-in-stockholm-solna-sweden-september-12-14-2022/

Nordic microscopy symposium – Save the date!

Please join the Nordic microscopy symposium on the 3^rd of October at the Live Cell Imaging core facility, Nikon Centre of Excellence at Karolinska Institutet. The symposium is organised by BergmanLabora, Ramcon Denmark and Inter Instrument AS. Please save the date.

The event will highlight Nordic research where light microscopy is a key tool.

Several Nikon fast super resolution systems will also be available: Nikon AX confocal with NSPARC and Nikon/CrEST V3 spinning disk with DeepSIM.

Before and after the symposium, the capability of these systems will be demonstrated during public sessions (on the 3^rd of October) and in private sessions (booking required) where you are welcome to bring your own samples.

Preliminary schedule:

Tuesday 3rd October

1000-1045 AX R NSPARC + CrEST V3 with DeepSIM public demonstration (in parallel)

1100-1145 AX R NSPARC + CrEST V3 with DeepSIM public demonstration (in parallel)

1200-1300 Lunch (requires pre-registration)

1300-1305 Welcome

1305-1345 *Keynote: TBC

1345-1410 *Nicoline Dorothea Daugaard (Dept. Biochemistry and Molecular Biology, SDU – Denmark):

Tracking T cells and their interactions with cancer cells in 3D using NIS-Elements General Analysis (GA3)

1410-1440 *LCI short talks:

Chiara Annunziata (Karolinska Institutet – Sweden)

Andrea Coschiera (Karolinska Institutet – Sweden)