Tag: Cool service

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, 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

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.

You’ll find more information here.

Don’t just sit on your bum!

In these strange Coronavirus time, one tends to sit at home in front of one’s computer. Following the Corona pandemics, it is not hard to predict a back ache pandemic!

I have been using Workrave for years and it has cured by shoulder ache! 🙂 Workrave is a freeware that can be downloaded from here.

Basically it locks your keyboard and mouse at the interval of time you decide and for how long as you decide. You can even set a maximum work time per day, a longer interruption for lunch or follow some simple stretching programs during the interruption.

I have simply set mine to lock my computer for 2 min every 30 min. Works a charm. 🙂

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.

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! 😀

Free genetic and image analysis tools

Here are a few image analysis tools (constructs for FRET, software…) that might be useful to you.

  • Construct for fluorescence biosensors and optogenetic tools
  • Free Image analysis software

http://www.hahnlab.com/tools/index.html

  • Free Image analysis software

https://www.utsouthwestern.edu/labs/danuser/software/

  • Free Image analysis software

http://cismm.web.unc.edu/

Party time at the LCI! :D

On the 10th of October, the Live Cell Imaging facility will have an open house and a little party to celebrate loads of great stuff:

  • The LCI turned 10 years old this year! 😊
  • We got a wonderful light sheet system earlier this year. It is high time to give it a name and splash it with a bit of champagne!
  • Gisele Miranda from Scilife/BII has joined the LCI team to help our users with image analysis
  • We got a great server/analysis capacity set up by the KI IT department

Wow! What a year! 😃

Please come and celebrate with us! If you do not know what our microscopy facility has to offer, it is time to be curious and pay us a visit.

  • Open house: drop in between 9:00-11:00
  • Baptising of the light sheet system and celebration of Gisele and our shiny new server: at 11:00

All this will happen on the 10th of October (next Thursday) at the LCI facility, on the 7th floor of Neo at KI Flemingsberg. Here you can see how to find us.

Please help us spread the news! 😊

How to identify cells and nuclei in an image?

NucleAlzer is a great new deep learning tool to identify roundish objects like nuclei and cells in fluorescent or bright field images.

To test if the tool works for you before you download it, you can simply upload one of your images and check the result. Easy! 😀

Call4Help: fast-track help with your image analysis project!

BII (BioImage Informatics, the great image analysis at SciLife Uppsala) and the LCI facility will run a new Call4Help on the 4th of September.

Anyone who is stuck with image analysis and wishes for quick help to build a pipeline should apply. You don’t have to acquire the images at the LCI. Anyone can apply.

How does it work? You first upload your images and a little explanation text. A few days later, we all meet virtually in a Zoom chatroom for a quick (30 min-1 h) online session. You get comments, suggestions and help with building a Fiji or CellProfiler analysis pipeline tailor-made for your images.

If you are interested, click on the link below to apply:

BioImage Informatics

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