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. ūüėä

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! ūüėÉ

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

Admin job related to microscopy at Euro-bioimaging Heidelberg

Here is a nice opportunity to change career if you feel like it and move to admin while keeping a strong microscopy feel.

Have a look at here.

ūüôā

 

CLIJ2: Open Computing Language and ImageJ2, GPU power for everyone

CLIJ2 allows you to use ImageJ/Fiji on GPU instead if CPU processing, so much faster! ūüôā

Here is a nice article about what CLIJ2 can do. By the way, this article is published on a new imaging forum called FocalPlane. Check it out! And here is the presentation of how to use CLIJ2 at one of the recent Neubias event in May 2020.

If you have an analysis pipeline built in Fiji, Icy or Matlab and processing takes a long time, CLIJ2 will help you a lot.

A microscopy facility job in Hamburg! :)

Researcher/ Light Microscopy Specialist (m/f/d)

UKE Light Microscopy Facility

Pay grade 13 TV-KAH

Work with your finger on the pulse in a compressed cosmos that is forever changing. A work environment where a person can make a difference because they have the space and environment to implement change and think differently.

*We offer*

  • Secure employment in an innovative and family-friendly university medical center in the middle of Hamburg (e.g. on-site kindergarten, free child care during school holidays).
  • Opportunity to participate in a wide range of further and additional educational training courses offered by the UKE Academy for Education and Careers, as well as a structured familiarization process.
  • Attractive pay structure as well as access to a high-quality health system
  • Opportunity to work at the best, state-of-the-art microscopes and to be involved in outstanding scientific projects

This position is initially limited for two years part as part of a project. An extension of this period is envisioned. This is a full-time position (38.5 h/week), which can also be filled with part-time models.

*What is expected of you*

  • Close collaboration with the UKE research community.
  • Developing latest imaging protocols and experimental designs
  • Trainings on different microscopy platforms
  • Organisation of light microscopy seminars and workshops
  • Securing maintenance and development of the core facility equipment
  • Supporting the operation of the core facility

*What we look forward to

  • Successfully completed studies in Natural Sciences with PhD, preferably in the area of Biophysics, Cell Biolology, Biochemstry, Microbiology, Bioengeneering or Biostatistics or comparable skills and capabilitie
  • Insights in and practical experiences with optical microscopy and imaging systems and latest microscopy techniques
  • Very good command of sample preparation techniques for light microscopy
  • Ability to teach non-specialists complex ideas
  • Experience in a dynamic working environment
  • Distinctive social competence, ability to act independently
  • Very good oral and written communication skills in English
  • Preferably experiences in the area of data analysis and quantification as well as programming skills (e.g. Matlab)

Contact person: Dr. Virgilio Failla Tel. +49 (0)40 7410 ‚Äď 51958/ E-Mail: a.failla@uke.de

We offer a work environment that offers everyone the same chances, regardless of age, sex, sexual preference, disability, ethnic background or religion. We are actively trying to increase the number of women in senior roles, especially in research and teaching. In the event of equal levels of qualification, preference will be given to female candidates.

The same rule will apply to all genders when one gender is deemed to be under-represented in the department relevant to the available position.

Severely disabled applicant with essentially identical technical and personal suitability will be preferentially selected.

We look forward to receiving your full application by the reference code

2020-321 until 29.6.2020.

Dr. Antonio Virgilio Failla

Head of Light microscopy facility

Universitätsklinikum Hamburg-Eppendorf

UKE Microscopy Imaging Facility (UMIF)

Campus Forschung (N27), EG, Room 00.108.2 Martinistraße 52

20246 Hamburg

Tel.:  (+49) 40-7410-51985

Mobil: (+49) (0)152-22815841