The first microscopy MOOC?

This MOOC for undergrad students by the University of Montpellier is about labeling and imaging vertebrate embryos.

All the videos are also available on their YouTube channel.

As far as I know, this is the first pure microscopy MOOC (Massive Open Online Course), dealing with sample preparation, imaging and data handling!

If you know of another microscopy MOOC (I know of some image analysis MOOC but not microscopy), please leave me a comment or sent me an email! 🙂

BII webinars and Global Bioimaging lectures

Lots of interesting courses and webinars about microscopy in these corona times. The BioImage Informatics facility at Scilife will present how useful it is to build imaging pipelines with Fiji/imageJ.

April 6th, 10:00-11:00: “ImageJ/Fiji – Make Your Own Macros – Overview”. This is not to teach how to script but to give you an overview of the scripting possibilities in ImageJ/Fiji. Please register here.

Version 2.0 of TissUUmaps is now released: TissUUmaps allows fast interactive display of tissue slide images and uses an overlay to display any sort of marker data on top. Be it spatially resolved gene expression, per cell data, or regions of interest. TissUUmaps is developed in the Wählby-Lab, with involvement of BIIF, and was first published in
Try out TissUUmaps and interact with a in-situ-sequencing dataset on a brain slice!

Advanced Methods in Bioimage Analysis, Online EMBO Practical Course, 26 Jun – 2 Jul 2021; Registration Deadline: 5 Apr 2021
This advanced course concentrates on teaching cutting-edge concepts and tools for quantitative image analysis, and will seek to upgrade the competencies of future bioimage analysis experts on both theoretical algorithm advancements as well as on practical implementation skills. BIIF is part of the scientific organization team. Register here.

Global BioImaging-ZEISS webinar series in Light Microscopy

Check here to see some nice general microscopy webinars by Global Bioimaging, the global pendant to Euro Bioimaging:

  • Tuesday, 30th March at 15:00 CEST: Introduction to Confocal Microscopy.
  • Tuesday, 20th April at 15:00 CEST: Multi-colour imaging – where are the limits & what are the opportunities?
  • Tuesday, 11th May at 15:00 CEST: Super-resolution: What is it? How can you do it? What does it enable?
  • TBA: From 2D to 4D imaging – how switching to a sheet of light has revolutionised volume acquisitions in Life Science.
  • TBA: Methods for Clearing your specimens – what are the options and which should you choose?
  • TBA: Automation in modern microscopy: easy ways to prevent costly accidents and enable your users with tools for easy experimental set up.

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!

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. 😊

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! 😃

Where to find microscopy jobs and wikis

Where to ask microscopy-related questions? 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.

Open source to build a custom made image analysis pipeline

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

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 for  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:


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 Forum to report Q&As and to welcome further questions/comments for each event.

You’ll 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.