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 https://doi.org/10.1093/bioinformatics/btaa541.
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.
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!
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!
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.
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
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.
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 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.
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.