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.
Tag: Learning
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. š
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, demosā¦ 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! š
Where to find microscopy jobs, forums 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, networkingā¦ 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 researchersā work conditionsā¦
Other places to look for work:
- Eurobioimaging
- European Microscopy Society (EMS)
- Indeed head hunter
- Simply Hired
- Nature Jobs
- KI Jobs
- ResearchGate
- Science jobs
- KI recruitment tool
- Professorpositions.com
- Academicum
- Confocal server
Microscopy wikis
– Kurt Thornās 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
– Microscopy Education by Olympus
– Microscopy Education by ZEISS
Freeware to turn widefield, TIRF or confocal images into super resolution images!
Check out this webinar tomorrow by Rickardo Henriques, the inventor of SRRF (surf), post processing magic for all types of images!
*Title:* Open and accessible cutting-edge technology forĀ super-resolution and machine-learning enabled microscopy
*When: *June 5th 4:00 pm CEST
*How to access/register*
And here’s a small teaser if you want to quickly see the topics we’ll cover.
Neubias webinars on Youtube
Updates on the next events of the NEUBIAS Academy@Home Webinar series,
Newly confirmed events:
5 May: ilastik beyond pixel classification, by Anna Kreshuk and Dominik Kutra-
6 May: GPU-Accelerated Image Processing with CLIJ2, by Robert Haase
7 May: Interactive Bioimage Analysis with Python and Jupyter, by Guillaume Witz
Upcoming events open to registration:
LAST CHANCE TO REGISTER:
28 April: Introduction to nuclei segmentation with StarDist, by Martin Weigert et al
29 April: Quantitative Pathology and Bioimage Analysis: QuPath v0.2.0, By Pete Bankhead
30 April: Advanced Image Processing with MorphoLibJ, by David Legland
Two weeks after the opening of the Academy and of the registrations, Webinars and online courses have already attracted over 5,000 registrations!
The events are recorded and some are already available on the Youtube NEUBIAS Channel.
Furthermore, a thread will be opened in the image.sc Forum to report Q&As and to welcome further questions/comments for each event.
Youāll find more information here.
Neubias online school of image analysis
Neubias is back with new ideas! Neubias is the Network of European Bioimage Analysts and what they burn for is to help scientists analyze their images.
Possibly inspired by the Corona time, they will start an online school for image analysis based on video tutorials and online events.
Have a look at their new page called Neubias academy where they announce several events coming up in the next few months.
Broadcasted lectures from the LCI microscopy course and private demos of light sheet and cameras
Our course starts tomorrow! š
Target audience:
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 and want to improve their skills.
Registrations are closed but all lectures are open to everyone without registration.
- The schedule and details of the venue are here.
- All lectures are also available online live. The link and instructions to watch are here.
- Make sure you check the schedule in case of last minutes changes.
If you are in Sweden, you are welcome to try some of the equipment on demo with your own sample.
To book at timeslot, please contact the responsible person directly.
- Light sheet microscope from M2Lasers: Valentina Loschiavo Valentina.Loschiavo(at)m2lasers.com
- Fast imaging of large sample
- Overview function to navigate in the sample and find the region of interest
- 800x800um field of view with 1um min resolution
- Any immersion media
- Sample size up to centimetres
- Wide Field microscope from Nikon with 3 different Andor cameras: Oliver Garner (oliver.garner(at)bergmanlabora.se)
- Nikon Ti2 microscope with 4 times larger field of view
- A front illuminated sCMOS camera: Good sensitivity and resolution, great speed, but a greyish background (Andor Zyla 4.2)
- A back-illuminated EM-CCD camera: highly sensitive camera with very dark background, but lower resolution and lower speed (Andor 897U)
- A back-illuminated sCMOS camera: same sensitivity and low background as an EM-CCD but better resolution and speed (Andor Sona)
The antibody validation nightmare
Ever wondered if that antibody you used throughout your whole PhD was actually also binding to something else than its supposed target protein?
Antibody validation in tissue staining is a very difficult task!
Here is a great step-by-step validation protocol published by EuroMabNet, a network of scientists who try to improve antibody validation.
And this paper gives a useful flow chart for antibody validation.
And here is the 5 pillars of antibody validation paper which explains what can be done to validate antibodies.
Know your RRid!
Imagine starting a study about some cool protein.
You find some useful articles on Google Scholar. In one paper, an antibody is mentioned. The name of the company that sold it to the authors is mentioned in the Material and Method but unfortunately that company has closed down or has been swallowed by one of the Pharma giants so you cannot order. Then you realize that the company was not producing any antibodies anyway, they were buying it from another company so there is no way to trace and buy the same antibody. Nightmare…
Then imagine that instead, the paper mentions the RRid number for that antibody. You do not know about what that is but you check and find this paper that explains it all.
Now suddenly, not only you can find on the Scicrunch website which company produces this antibody and which resells it so you can buy it, but you can also search pubmed for the RRid and find all the articles that mention it, opening your eyes to lots of results about your protein that have been published specifically with using that antibody. Now you can also check if the antibody gives consistent results!
And imagine being to do this for your favorite mouse model as well. See all publications that have mentioned your mouse RRId!
But it relies on you writing the RRid of your antibody or mouse in your next publication so think about it! š