Images

The LCI microscopy course 2021 starts next week! :)

As usual the lectures at the LCI microscopy course will broadcasted live online, free of charge and there is no need to register.

Title: Microscopy: improve your imaging skills – from sample preparation to image analysis

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.

Applications are closed but all lectures will be broadcasted live and open to anyone without registration.

The course covers the following topics:

  • Optics, image formation, fluorescence, fluorophores, microscope and microscopy types
  • Objectives and refraction index, Cameras and detectors
  • Noise and background, Cameras and detectors, Bit depth and saturation, Multicolour imaging
  • Resolution and contrast, Sample preparation, Immunostaining
  • Nyquist sampling, Confocal and wide field settings, Scaling up and speeding up, High throughput/content
  • Volume imaging, deconvolution, multiphoton, Clearing and expansion
  • Live cell imaging, Fourier, AI, Super Resolution microscopy
  • Data handling, OMERO.figure, Requirements for image analysis, Colocalization
  • Image processing and analysis

Check the course schedule and details of how to join the Zoom webinars. Scroll down to read the kind testimonies of our dear students! 😊

Here is the course syllabus.

Hope you enjoy the LCI facility microscopy course 2021!

Gisele got the Chan Zuckerberg Initiative grant!!

Congratulations to our dear in-house image analyst Gisele Miranda who got the prestigious Chan Zuckerberg Initiative grant in December! 🙂

Gisele got this grant thanks to the fruitful collaboration between the BioImage Informatics facility at Scilife and the Live Cell Imaging facility at KI. We are delighted for her and for all the LCI users as this will allow us to keep working with Gisele for many years.

Congratulations Gisele! Very well-deserved! 🙂

Look at what CZI has chosen as their symbol of Science: a microscope!

5 webinars on Big Data

God fortsättning everyone! Happy New Year! 🙂

Neubias is back with great image analysis/handling webinars!

Here are 5 webinars with interesting information about how to handle Big Data.

 

From Images to Knowledge virtual workshop

Nov 30th-Dec 2nd, Janelia Research Center organizes a great image analysis workshop with loads of goodies. Everything is online and free. There are in depth and more general workshops about Deep Learning with different freeware, programming and scripting of all sorts, Big data things… Check the program here.

Super resolution course and webinars at ALM

Dear all

See here for more details about the ALM super resolution microscopy course in January. Note that the webinars are open to everyone (see registration email at the bottom of the page) and are always very interesting talks. 😊

Microscopy facility jobs in Europe :)

One in Denmark, one in Italy, one in France/Singapore and in Germany!

 

 

LCI microscopy course, vintage 2021 :)

The Live Cell imaging facility will run again its intensive light microscopy course in Jan-Feb 2021.

The schedule can be found here.

As usual, all lectures will be publicly broadcasted live. So if you think that a lecture could be useful for you, you are welcome to listen, without registration, by following this link.

Due to the current pandemics, only registered students will be allowed in the lecture room.

The course comprises lectures, workshops, imaging of your own sample, demos… It will run 26 Jan-12 Feb, 3 days/week (tues-thurs) 9:00-17:15.

There are only 16 spots. The course counts for 6 credit points.
The rest of the time (the course counts for 4 weeks) is used for home assignments. Mondays and Fridays will also be used for individual workshops where we image your own sample.

The application process is open now until the 16th of November. Please read carefully the eligibility criteria. You will need to sent me some images of your sample at the time of application. This course is only open to people who already have some experience of fluorescence microscopy.

Microscopy: improve your imaging skills – from sample preparation to image analysis

At the end of the course, the participants will be able to:
1- Describe the difference between wide field, confocal and light sheet microscopes as well as the different types of confocal microscopes and choose which system is most suited to their experiments
2- Pick the best combination of fluorophores for their experiment by matching their spectra with the microscope light source and filters, identify and eliminate bleed-through and cross-excitation problems
3- Explain objective specifications and limitations and choose the appropriate objective for their own experiments
4- Describe how to fix, mount and handle their sample in a way that is optimal for imaging
5- Find their sample and the area of interest without bleaching it
6- Adjust the condenser for proper DIC imaging (Koehlering)
7- Explain how to set the following parameters on a wide field, a confocal or a light sheet system to best match the requirements of their sample and reliably answer their scientific question: resolution, pixel size, averaging, scan speed, illumination power, detector gain and offset, camera readout rate, exposure time and camera binning
8- Explain which applications require a hardware or a software autofocus, a spectral detector, a resonance scanner, two-photon or super resolution microscopy
9- Explain the advantages in using the automation of a microscope system to collect multidimensional data
10- Explain how to deal with images before publication in scientific journals
11- Describe the imaging requirements for automated image analysis
12- Run an image analysis pipeline on freeware (ImageJ/FIJI, Cell Profiler) designed for their own images and scientific question.

Please spread the word to your colleagues.

We are looking forward to meeting you and your sample! 😃

2 microscopy jobs in Europe! :)

·        Light microscopy core facility support specialist, Biomedicum Imaging Unit, University of Helsinki, Finland
direct link to this job offer
closing date 10 October 2020

·        Bioimage Analyst, CFIM, University of Copenhagen, Denmark
direct link to this job offer
closing date 4 October 2020

Tweety turned into a power machine!

Our dear Tweety microscope, which was simplest and cutest of all the LCI systems, has muted into our most sophisticated power machine!

On the 24th at 10, we will run an online demo (link below) to show what our upgraded Tweety can deliver:

  • Much larger field of view (from 18 mm diagonal to 25 mm)
  • Upgraded single point confocal on the left side
  • Resonant scanner with 1024×1024 pixels (compared to 512×512 on our other resonant scanners), still the same speed (30 fps) and improved low noise
  • Spinning disk confocal on the right side with bypass to image wide field
  • 2 very sensitive cameras on the right side: one with the very large field of view and 11um pixels for best sensitivity and one with the normal field of view and 6.45 pixels for best resolution
  • Our great Primo is still on the back of the microscope to allow micropatterning of proteins at the bottom of a dish or micromanufacturing of wells in the shape/pattern of your choice
  • 2 wonderful silicon immersion objectives specialized for tissue imaging with automatic correction ring: 20x/1.05 and 40x/1.25

After the demo, the LCI users who have already been trained on our widefield systems can get access to Tweety for free after a mandatory short training.

Please add the demo in your calendar and make sure to test the link ahead of the meeting.

Link to the Zoom Meeting on the 24th at 10am: https://ki-se.zoom.us/j/7302561100

Where to find microscopy jobs and wikis

Where to ask microscopy-related questions?

– Image.sc and microlist
Post your microscopy, sample preparation and image analysis questions

– Confocal server
Old email-based forum that is followed by tons of people across the globe as well as most microscopy companies. Post your microscopy and sample preparation questions.

Freeware for image analysis

– Image J/Fiji
Great freeware to open images acquired on any microscope, resize, crop, change contrast, create movies, annotate, analyze and much more.

– Cell Profiler
Freeware for automated image analysis including machine learning.

– KNIME
Open source to build a custom made image analysis pipeline

– Icy
Great freeware to open images acquired on any microscope, resize, crop, change contrast, create movies, annotate, analyze and much more.

Networks, jobs and career

Light microscopy jobs, meetings, courses, networking… in Europe. Remember to mail them that you want to show up on their map of European microscopy!

Loads of information from which companies/institute works with research to how to find an apartment when moving to another lab, find work, know your rights, express your opinion about researchers’ work conditions…

Other places to look for work:

Microscopy wikis

– Kurt Thorn’s excellent microscopy blog
I highly recommend this blog even if it is not updated anymore. Monthly digest of major microscopy related articles. Loads of tips.

– Microscopy Education by Nikon

– Leica Science Lab

– Microscopy Education by Olympus

– Microscopy Education by ZEISS

– Molecular Expressions

– SVI deconvolution

– Microscopy info

– Nature Milestones Light Microscopy

– iBiology Microscopy Course