Nikon Europe recruits an image analyst in Leiden.
See here if this is the dream job for you. 🙂
Tag: Image analysis
BII webinar about a great tool! TissUUmaps
The BioImage Informatics facility at Scilife organizes a new presentation on free and open-source tools: TissUUmaps, a browser-based tool for GPU-accelerated visualization and interactive exploration of millions of datapoints overlaying tissue samples.
Users can visualize markers and regions, explore spatial statistics and quantitative analyses of tissue morphology, and assess the quality of decoding in situ transcriptomics data. TissUUmaps provides instant multi-resolution image viewing, can be customized, shared, and also integrated in Jupyter Notebooks. TissUUmaps was created in collaboration between BIIF and the Wählby lab. You can read more about it and test the software on its web page: https://tissuumaps.github.io/
During the seminar, we will go through basic usage of TissUUmaps: installation, loading images, markers and regions, change visualization settings, and how to load / save / share projects. The webinar will be given by Christophe Avenel and will take place on March 3rd, 09:00-10:00 (instead of our normal Call4Help session). There will be time for questions and discussion, so we hope this event to be very interactive. Please register here.
The LCI microscopy course 2022 is now open for registrations!
It is now time to apply to the intensive LCI microscopy course Jan/Feb 2022: 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 their knowledge is limited.
All the lectures at the LCI microscopy course will also broadcasted live online, free of charge and there is no need to register.
All details about the course including course schedule, how to apply, and how to follow the lectures are found here.
Scroll down to read the kind testimonies of our dear students! 😊
Hope you enjoy the LCI facility microscopy course 2022!
2 Bioinformatician jobs at Scilife lab
The BioImage Informatics facility is our favorite image analysis facility at ScilifeLab! 🙂
They are looking for 2 bioinformatician working with microscopy images. Here is the first job ad. And here is the second one.
Please spread the word! 🙂
Online image analysis course
You can join the Switzerland’s Image and Data Analysis School, ZIDAS 2021.
This one-week school provides a hands-on introduction to image processing and analysis, with an emphasis on biologically relevant examples.
This school is for you if…
* you are a life-science researcher with a pressing need to quantify your light-microscopy images.
* you are uncertain about how to: Best calculate co-localisation, do deconvolution, automate the counting of cells, track objects over time, handle massive amounts of image data, record your image-analysis workflows in a reproducible manner.
More information can be found here: https://2021.zidas.org/
What can Artificial Intelligence do for you?
Check out the Nikon Artificial Intelligence (NIS.ai) webinar series to understand how Ai can help you in your microscopy experiments.
The NIS.ai Webinar Series will take place on Tuesdays at 14:00hrs and we are delighted to announce the first two talks:
- June 29th 14:00 – Dr Carlo Beretta from Heidelberg University on “How to build a Bioimage Analysis Workflow with multiple image analysis tools”
- July 6th 14:00 – Dr Marko Popovic from Nikon Centre of Excellence in Amsterdam on “Quantitative pathology”
Program and free registration: here.
Artificial Intelligence tools
Artificial Intelligence, Deep Learning and Neuronal Networks are taking over the world, including microscopy. Within the next couple of years, you might well end up wondering how you got anything done without them!
Having an idea how Artificial Intelligence, Deep Learning and Neuronal networks work means that you will be able to come up with ideas about how they can help you in your research.
The Neubias (Network of European image bioanalysts) webinars and meetings are a good place to learn.
Here are 2 upcoming webinars about tools to train and use AI algorithms.
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 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.
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!
Gisele got the Chan Zuckerberg Initiative grant!!
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!