Python4BIA (3-Day Distributed Course)
Python scripting provides a general and flexible toolset for researchers to quantify and analyse digital images acquired from microscopy or clinical imaging. It enables researchers to automate image processing and connect their workflows with downstream processes like statistical testing and data visualisation.
This 3 day workshop begins with an introduction to python language essentials and uses image data to familiarise participants with core programming concepts in a research-relevant manner. Participants will learn to use popular python libraries such as scikit-image, matplotlib and pandas to visualise, interact with and extract quantitative data from digital images. The course will also cover the use and programmatic access to Napari, a powerful n-dimensional viewer.
Over the course, participants will be familiarised with practical bioimage analysis techniques, how various image processing operations work and when to perform such operations. You will learn how to segment images (identify object of interest in their images), using classical methods as well as machine learning solutions. Finally, you will be able to quantify and visualise biologically interesting properties such as quantity, intensity, or morphology of their objects of interest.
Call4Help
Call4Help is a bi-monthly public consultation session organized by the DBI-INFRA Image Analysis Core Facility. You can attend these sessions to obtain quick guidance for your bioimage analysis problems and learn from the questions of other peers.
Call4Help
Call4Help is a bi-monthly public consultation session organized by the DBI-INFRA Image Analysis Core Facility. You can attend these sessions to obtain quick guidance for your bioimage analysis problems and learn from the questions of other peers.
Call4Help
Call4Help is a bi-monthly public consultation session organized by the DBI-INFRA Image Analysis Core Facility. You can attend these sessions to obtain quick guidance for your bioimage analysis problems and learn from the questions of other peers.
Call4Help
Call4Help is a bi-monthly public consultation session organized by the DBI-INFRA Image Analysis Core Facility. You can attend these sessions to obtain quick guidance for your bioimage analysis problems and learn from the questions of other peers.
Call4Help
Call4Help is a bi-monthly public consultation session organized by the DBI-INFRA Image Analysis Core Facility. You can attend these sessions to obtain quick guidance for your bioimage analysis problems and learn from the questions of other peers.
Call4Help
Call4Help is a bi-monthly public consultation session organized by the DBI-INFRA Image Analysis Core Facility. You can attend these sessions to obtain quick guidance for your bioimage analysis problems and learn from the questions of other peers.
Image Analysis Open Office
The DBI-INFRA Image Analysis Core Facility will be visiting the Danish Molecular Biomedical Imaging Center (DaMBIC) at the University of Southern Denmark to provide free consultation sessions for life scientist with bioimage analysis questions.
Our team will provide you with guidance on your bioimage analysis problems and you will also have a chance to learn from the questions of your peers.
Python4BIA
Python has quickly become the universal language for scientific computing and deep learning applications.
During this 2 day workshop, we will cover Python programming essentials and rapidly progress to practical bioimage analysis techniques through interactive, hands-on sessions. You will also learn how to utilize and programmatically access Napari, a powerful nD viewer; and deploy and train foundational bioimage analysis deep learning models such as U-NET and Cellpose.
The workshop includes dedicated time for participants to work with their own images, applying newly acquired skills under teachers supervision.
Call4Help
Call4Help is a bi-monthly public consultation session organized by the DBI-INFRA Image Analysis Core Facility. You can attend these sessions to obtain quick guidance for your bioimage analysis problems and learn from the questions of other peers.
Call4Help
Call4Help is a bi-monthly public consultation session organized by the DBI-INFRA Image Analysis Core Facility. You can attend these sessions to obtain quick guidance for your bioimage analysis problems and learn from the questions of other peers.
Call4Help
Call4Help is a bi-monthly public consultation session organized by the DBI-INFRA Image Analysis Core Facility. You can attend these sessions to obtain quick guidance for your bioimage analysis problems and learn from the questions of other peers.
Call4Help
Call4Help is a bi-monthly public consultation session organized by the DBI-INFRA Image Analysis Core Facility. You can attend these sessions to obtain quick guidance for your bioimage analysis problems and learn from the questions of other peers.
Call4Help
Call4Help is a bi-monthly public consultation session organized by the DBI-INFRA Image Analysis Core Facility. You can attend these sessions to obtain quick guidance for your bioimage analysis problems and learn from the questions of other peers.
Call4Help
Call4Help is a bi-monthly public consultation session organized by the DBI-INFRA Image Analysis Core Facility. You can attend these sessions to obtain quick guidance for your bioimage analysis problems and learn from the questions of other peers.
Image Analysis Open Office
The DBI-INFRA Image Analysis Core Facility will be visiting the Aarhus University Bioimaging Core Facility at the Institute of Biomedicine to provide free consultation sessions for life scientist with bioimage analysis questions. Our team will provide you with guidance on your bioimage analysis problems and you will also have a chance to learn from the questions of your peers.
Call4Help
Call4Help is a bi-monthly public consultation session organized by the DBI-INFRA Image Analysis Core Facility. You can attend these sessions to obtain quick guidance for your bioimage analysis problems and learn from the questions of other peers.
Call4Help
Call4Help is a bi-monthly public consultation session organized by the DBI-INFRA Image Analysis Core Facility. You can attend these sessions to obtain quick guidance for your bioimage analysis problems and learn from the questions of other peers.
Call4Help
Call4Help is a bi-monthly public consultation session organized by the DBI-INFRA Image Analysis Core Facility. You can attend these sessions to obtain quick guidance for your bioimage analysis problems and learn from the questions of other peers.
Call4Help
Call4Help is a bi-monthly public consultation session organized by the DBI-INFRA Image Analysis Core Facility. You can attend these sessions to obtain quick guidance for your bioimage analysis problems and learn from the questions of other peers.
Danish Bioimaging Symposium
The Danish BioImaging Scientific Symposium will be held in Copenhagen on the 24th – 25th of June at the Faculty of Health and Medical Sciences, UCPH.
This is a unique opportunity to network with the Danish BioImaging community, learn about the latest bioimaging technologies, and share your latest image-based research.
IMAGE ANALYSIS COURSE
We will initially use Fiji to illustrate fundamental image analysis concepts, then expand to introduce other software packages such as QuPath and Napari.
The students will learn what a digital image is, how and when to perform basic image processing tasks and how to combine such tasks to perform advanced image processing and segmentation, automated pixel classification and 2D and 3D measurements. Furthermore, the students will learn basis Macro programming and how to automate analysis of many images.
Sign up COPENHAGEN IMAGE ANALYSIS PHD COURSE | Sign up (ku.dk)
Learning objectives
A student who has met the objectives of the course will be able to:
Use open source tools (Fiji, Cell Profiler and others)
Do basic Macro programming in Fiji (ImageJ) for automated batch analysis of images
Understand the principles of image processing and analysis
QuPath workshop
Are you interested in QuPath for digital pathology?
If so, join us at the University of Aarhus for this free one day workshop (limited seats available)!
During this hands-on workshop organised on wednesday 17 April 2024, participants will be introduced to QuPath, a powerful user-friendly bioimage analysis software designed to extract quantitative information from microscopy images. QuPath is optimised to process whole slide images from digital pathology, but it can also handle 2D images acquired by most fluorescence microscopes. Common uses include the identification, measurement and classification of nuclei, cells and regions of interest in the images.
Python4BIA Workshop (2nd edition)
Python quickly became the lingua franca for scientific computing and the recent development of deep learning algorithms. During this 2 day workshop (which does not assume any prior programming knowledge), we will cover Python language essentials and quickly ramp up to bioimage analysis techniques in a hands on fashion. The next segment of the course covers the use and programmatic access to Napari, a powerful nD viewer, and the deployment and training of foundation bioimage analysis deep learning networks such as U-NET and Stardist.
Quantitative 3D Bioimaging PhD Course
Learn how to quantitatively address spatial biomedical research questions using two- and three-dimensional microscopy and image analysis. This 5-day intensive residential course includes lectures on how to design and run quantitative imaging pipelines and publish the results, inspirational research talks, and demo workshops in laser scanning & spinning disc confocal microscopy and image analysis.
Python4BIA Workshop
Python quickly became the lingua franca for scientific computing and the recent development of deep learning algorithms. During this 2 day workshop (which does not assume any prior programming knowledge), we will cover Python language essentials and quickly ramp up to bioimage analysis techniques in a hands on fashion. The next segment of the course covers the use and programmatic access to Napari, a powerful nD viewer, and the deployment and training of foundation bioimage analysis deep learning networks such as U-NET and Stardist.
Bridging Nordic Microscopy Insfrastructure Symposium (BNMI 2023)
The second meeting of the Bridging Nordic Microscopy Infrastructures (BNMI) network took place at the University of Southern Denmark in August 22-25. The aim of the meeting was to bring together scientists who develop or utilize biological imaging methods, the Nordic imaging core facilities, and representatives of industry to discuss projects and present the latest imaging technologies. Read more about the event on the BNMI website. 
BioImage Analysis PhD Course
This PhD course consists of a preparation (June 16) on Image formation and ImageJ basics, followed by 5 day course (June 19-23) on image analysis (filters, pixel & object classification, object segmentation). It covers several widely used applications (ImageJ, QuPath, CellProfiler, Napari) and an introduction to programming and automation to assemble algorithms into advanced image analysis workflows. Time will also be allocated to apply what you learned on your own data. Please find more info here and register here (participation cost: 2.500 Kr).
QuPath Workshop
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