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Events and workshops

Events Spring 2024


Mar 14: LU eScience Hub presenting the Swedish infrastructure InfraVis – visualisation experts at your service

InfraVis is a Swedish national infrastructure that provides advanced visualisation services on research data from any scientific domain. Effective as of 2022, InfraVis aims at supporting Swedish scientific advancement and is funded by the Swedish Research Council.

Lund University is one of the nine Swedish universities forming the InfraVis constellation that with Chalmers as lead partner got national infrastructure funding from the Swedish Research Council. The Infravis@LU Team draws upon the breadth of knowledge at LU, with key elements being located in four faculties and is coordinated by the LU Research Infrastructure ‘Correlative Image Processing and Analysis’ (CIPA)

This event is particularly geared to address users needs in infrastructures such as MAXIV, ESS, LINXS as well as the Medical, Engineering and other faculties working with data and in need of machine learning and visualisation expertise at Lund University.

Deadline for registration: 11 March 12:00 (noon)

Organizers:

  • InfraVis – The National Research Infrastructure For Data Visualization
  • CIPA – The research infrastructure for Correlative Image Processing and Analysis
  • eSSENCE and eScience – the LU eScience Hub at Lund University

Programme:
13:15 Alexandros Sopasakis – welcome on behalf of the LU eScience hub
13:20 Emanuel Larsson, Node Coordinator for InfraVis & CIPA: "Introducing InfraVis @LU and application experts"
13:35 Jonas Lindemann, LUNARC & InfraVis: "Visualising dams with Python and ParaView"
14:00 Joakim Eriksson, Ergonomics and Aerosol Technology, VR Lab & InfraVis: "VR-lab at the Department of Design Sciences"
14:25 Jonas Ahlstedt, Lund University Bioimaging Centre, LBIC, CIPA & InfraVis: "Preparing and exploring 3D imaging datasets from the Life Science field in Virtual Reality"
15:00 Fika and mingle


Feb 29, Workshop: Human Perception and Advanced Visualization of 3D Medical Imaging Data

29 February, 12.30 -16.30, University of Copenhagen,

This interactive workshop aims to guide researchers in crafting impactful visualizations that enhance comprehension and communication of complex findings. The workshop encourages active participation from researchers interested in refining their skills and staying up to date with the latest advancements in visualization technologies. By the end of the event, participants will gain practical insights, enabling them to create visually compelling representations of their 3D imaging data and foster clearer communication and deeper understanding of their research findings. The workshop targets both 3D image data from clinical scanners and data from preclinical imaging of micro and nano-imaging systems like synchrotrons.

The workshop will be held at the University of Copenhagen (Faculty of Science) and the organizers of the event are in addition to HALRIC:

  • QIM – Center for Quantification of 3D Imaging data from MAX IV
  • InfraVis – The National Research Infrastructure For Data Visualization
  • DBI – Danish BioImaging Network
  • LINXS – Institute of Advanced Neutron and X-ray Science
  • CIPA – The research infrastructure for Correlative Image Processing and Analysis

Events Fall 2023


Nov 8 2023, LUNARC training: Matplotlib for Publications

From: 2023-11-08 10:00 to 15:00

Matplotlib is among the most popular and advanced function libraries for the production of journal-quality data visualisations, with extensive, often under-utilised resources to make figures both richer in content and easier on the eye. In this course, participants will learn the finer details of producing figures for publication with Matplotlib, including tips on:

  • how to choose plot types based on the quantity and distribution of data
  • how to legibly display multiple sets of data or models on the same plot, and customise cycling through distinguishing features
  • how (and why) to choose fonts and colors to accommodate common visual impairments
  • how to customise axis label formats and tick locations
  • how to standardise plot settings with rcparams.

This course consists of two lectures with demonstrations via Jupyter notebooks, and two exercise sessions for students to practice with prepared data. The course will be taught in English via zoom.

Instructor: Rebecca Pitts (application expert at LUNARC, PhD in Astronomy) will be the principal instructor.

Registration: For more information and registration, please visit the LUNARC event page.


Sept 18 2023, 14:30 - 16:30 | Meet CIPA and AI Lund at International Forum for Computer Vision in Ecology and Evolutionary Biology

Representatives of CIPA

Join the talks given by CIPA and AI Lund on the first day of the forum and learn about image analysis and visualization expertise and opportunities at Lund University. 

Image Analysis and Visualization support at Lund University by Emanuel Larsson, CIPA.

The advancement of imaging techniques both in 2D, 3D and 4D requires large amounts of data sets to be analyzed and visualized. During this talk I will present 3 imaging platforms and infrastructures where Lund University is a partner, including highlighted user projects and pedagogic training methods.

CIPA (Correlative Image Processing and Analysis)  - a local research infrastructure at Lund University with the aim of reducing the gap between the amount of acquired and consequently analysed images.
InfraVis - a national research infrastructure for data visualization from any scientific domain and modality, including 9 Swedish partner universities.
QIM (the Center for Quantification of Imaging Data from Max IV) - a cross-border collaboration platform for 3D/4D imaging at large-scale imaging facilities, aimed at developing algorithms for quantitative image analysis.

Building Autonomous Image Analysis Systems for Applications in Ecology by Alexandros Sopasakis, CIPA.

The increasing access to autonomously operated technologies offers vast opportunities to sample large volumes of biological data, including image data. However, these technologies also impose novel demands on ecologists to apply efficient tools for data management and processing. 

We discuss a couple of specific approaches and machine learning methodologies and tools which can help enable efficient, real-time processing of large amounts of image or video data. We present these methodologies within the context of two distinct ongoing research projects. The first project involves the processing of image and video data obtained from subsea environments, contributing to the realms of marine ecological research and monitoring. Additionally, on the next project, we delve into the application of the proposed methodologies towards identification and quantification of beta-glucan within tomography images of seeds.

Combining Image Analysis and Visualisation in Blender 3D by Jonas Ahlstedt, CIPA.

The increasing use of Blender in the scientific community has spurred the development of several tools useful in image analysis and visualisation - especially within the life sciences. Besides obvious cases such as using Blender as a tool for preparing data for 3D-printing, the built-in unbiased raytracer (Cycles) provides excellent means for visualising large and complex datasets with high fidelity. Even more interesting, the built-in tools present many opportunities for performing quantitative analysis in many different ways.

In this live demonstration we will see some project examples of combining image analysis and visualization in a few projects from different fields and discuss the possible future of using Blender as a scientific tool.


Sept 18 - 22 2023 | International Forum for Computer Vision in Ecology and Evolutionary Biology

The Department of BiologyCIPA and AI Lund at Lund University invite you to the International Forum for Computer Vision in Ecology and Evolutionary Biology to explore with us how computer vision can be used to break ground in the fields of ecology and evolutionary biology. The forum combines symposia, consisting of presentations by international experts, with workshops, group discussions and social events to advance the use of computer vision among evolutionary ecologists, and to promote networking and collaboration among participants.   

When: 18th - 22nd September, 2023

Where: Ecology building, Lund University

Register by 15th June

Speakers

Events Spring 2023

COMPUTE Courses in Scientific Computing and Visualization

Scientific Computing with Python and Fortran

HT 2023, 1.5 ECTS

Target audience: Students with basic knowledge of programming in any language who would like to learn the techniques of scientific programming. 

Course content: Scientific programming in Python, including writing numerical codes with NumPy, data handling, visualisation with Matplotlib and ParaView, writing user interfaces with Qt, creating Python environments for scientific applications, using the compiled language Fortran - stand-alone or via mixed-language programming with Python.

Read more and share the information with those who might be interested.

Basic Data Handling and Visualization with R

HT 2023, 1.5 ECTS

The course focuses on data management and visualization, and it aims to provide basic knowledge of the R programming language to facilitate the independent use of tools written and/or implemented in this language, such as statistical analysis packages. 

Course content: Importing data into RStudio/Posit, summarizing data, creating new data, cross-referencing, merging data, selecting appropriate, graphically appealing charts in different formats, and exporting data and charts in different formats. 

Read more and share the information with those who might be interested.


Apr 17 - 19 2023 | Workshop on Data Visualization in R - Lund

Organized by NBIS – National Bioinformatics Infrastructure Sweden

A national course open for PhD students (prioritized), postdocs, researchers and other employees within Swedish universities who are interested in learning to produce publication quality plots using different packages in R.

Where: Retina D227, Biologihuset
Sölvegatan 35, Lund, 223 62

Contact: edu [dot] plotting [dot] r [at] nbis [dot] se (edu[dot]plotting[dot]r[at]nbis[dot]se)

Read more about the syllabus, entry requirements and fee.

Apply before 31st March.


Feb 15 2023 | Spectroscopic Data Processing and Analysis 

Lunch webinar + a case study workshop  

Curious about spectroscopic techniques and hyperspectral imaging? Join this CIPA webinar demonstrating how to solve practical problems in spectroscopic data analysis.

Examples include: 

-Correction for water vapor and scattering effects in FTIR  
-Step discontinuities in O-PTIR 
-Identification of wavenumbers of interest in Raman spectra  
-Visualization of weak but significant components in hyperspectral (IR-visible) images 
-Image analysis and classification. 

Carl Troein. Portrait photo.

The webinar will be held by Carl Troein, computational biology researcher and 2D Spectroscopy analysis expert at CIPA - the Correlative Image Processing and Analysis software infrastructure at Lund University.  

The webinar will be followed by a non-compulsory case study workshop where you have the opportunity to discuss issues in your spectroscopic data with Carl Troein. 

Target audience: Everyone using spectroscopic methods or analyzing spectroscopic data, especially for imaging in two dimensions. 

Where: Zoom. Registration required.

When: 15th February 

Lunch webinar: 12:00 – 13:00 / Case study workshop: 13:00 – 15:00
Select an available time slot in the registration form. Only one participant/project per time slot.  

Register by 13th February.


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Past Events

Events 2022


Oct 24-26 2022 | Lund Visualization Week

Join Lund Visualization Week arranged by the Lund University node of InfraVis and by CIPA - the InfraVis@LU coordinating unit. Explore data visualization opportunities in a variety of research areas, from natural sciences to humanities.

Visualization of an eye. Illustration.

Visualization of single-cell gene expression, identification of environmental disasters through visualization, using visualization to explore the relation between language use and motion as well as visualization with Blender and Paraview. This is just a taste of the presentations and hands-on workshops you can expect at Lund Visualization Week. 

Where: VR Lab at Ingvar Kamprad Design Center, Sölvegatan 26, 223 62 Lund
When: 24th - 26th October, 2022.

Detailed programme:

Monday
10.00-11.00. Visualizing the Past: the Use of 3D Recording Technology in Support of Archaeology (Nicolò Dell’Unto)
11.15-12.00. Virtual Reality Lab Tour (Joakim Eriksson & Mattias Wallergård)
13.15-15.00. Workshop: Learn to visualize with Virtual Reality! (Joakim Eriksson & Mattias Wallergård)

Tuesday
9.15-10.00. How can visualization be used in outreach? (Pontus Wiahl & Louise Andersson, Wisdome Malmö – a venue for visualization with a 360 degree dome theater and digital labs.)
10.15-11.00. Visualizing data from satellites observation systems for identifying environmental disasters and improving food production (Alexandros Sopasakis)
11.15-12.00. Visualising results in the numerical toolbox DUNE (Robert Klöfkorn)
13.15-15.00. Workshop: Create your own animations with Blender (Jonas Ahlstedt)

Wednesday
9.15-10.00. Seeing language: Using visualization to explore the relation between language use and motion (Marianne Gullberg and Henrik Garde)
10.15-11.00. How can AI/ML support visualization? (Kalle Åström)
11.15-12.00. CellexalVR – a VR platform for the visualisation and analysis of single-cell gene expression data (Shamit Soneji)
13.15-15.00. Workshop: Visualising Scientific data using ParaView (Jonas Lindemann)

Find out what Lund Visualization Week was like


Oct 28 2022 | Stakeholder meeting: Digital platforms

Join this Stakeholder Meeting to share experiences and views on how we can work together for better science and innovation in the field of bioimage analysis. Stakeholder meeting is arranged by QIM, Danish Bioimaging Network and Alexandra Instituttet.

More info and registration


Sept 5-6 2022 | InfraVis Meeting Days, Uppsala

Carl Troein. InfraVis

InfraVis staff are all gathering at Ångström Laboratory in Uppsala to discuss crucial points for the successful functioning and development of InfraVis, including a review of the progress of pilot projects. Outcomes of the event will be become available here, in the News section. In the meanwhile, you can check the InfraVis website for more information. 


March 15 2022, 09.00-13.00 | CIPA Expo 2022 

Correlative Image Processing and Analysis (CIPA) invites you to the first annual CIPA Expo 2022 to be held at Pufendorf. 

The event will include

-presentations from the CIPA coordinator and application experts as well as from an affiliated application expert for single-particle cryoEM software/hardware at Lund University. 
-presentations about workstations and software available at CIPA
-use case / user story presentations
-tomography and  spectroscopy analysis
-LUNARC resources for image analysis and processing
-the new national Research Infrastructure 'InfraVis' and artificial intelligence for image processing and analysis.

Sign up using the registration link
Deadline for registration: 11 March

See the attached programme for details: CIPA EXPO 2022 PROGRAM (PDF, 119 kB, opens in a new tab)


Events 2021


June 18 2021  | Workshop - Image analysis beyond borders 

Workshop - Image analysis beyond borders

A workshop about both resources for imaging and analysis, but also for science cases. Stay for the virtual theme session, bring your own questions up for discussion, display a digital poster, or just mingle and hang around in the virtual meeting space REMO where you can listen to discussions around different tables and view posters.

Organized by HALOS-QIM-CIPA-CSSB!

For more information visit https://www.halos.lu.se/calendar/workshop-image-analysis-beyond-borders


June 2021 | Mondays with MATLAB - Using MATLAB in an HPC environment

A three series workshop on parallel computing, Machine Learning, and Deep Learning using large compute resources.

With MATLAB and the MATLAB Parallel Server, researchers can use the familiar MATLAB environment to run computationally intensive MATLAB programs efficiently on computer clusters. This event will introduce participants who are familiar with the MATLAB environment to the MATLAB Parallel Server and show how to run batch jobs, parallel computations, and provide insights into the caveats in running in a cluster environment. The event will also show how to use the built-in capabilities for Machine Learning in MATLAB using the MATLAB Parallel Server and how to do deep learning with MATLAB using modern GPUs on a cluster computer through the MATLAB Parallel Server. 

The seminars will be given from 9.00 to 17.00 on three consecutive Mondays in June 2021

https://www.lunarc.lu.se/training/mondays-with-matlab-june-7-14-21-2021/


January 13-15 2021 | Amyloid Workshop: User-friendly analysis of spectroscopy data with Quasar - multivariate statistics and machine learning

LINXS, in collaboration with the SMIS beamline at SOLEIL and the Biolab from the University of Ljubljanais organising a 3-half day hands-on workshop to introduce the QUASAR software, to address the infrared user community's need for a user-friendly and open-source software for data analysis.

This 3-half day hands-on training will be fully digital during January 13-15, 2021.

For more information:
https://www.linxs.se/events/2020/2/11/linxs-event-workshop-user-friendly-analysis-of-spectroscopy-data-with-quasar-multivariate-statistics-and-machine-learning


Events 2020


November 18 2020 | 13:00 - 17:00| Workshop on vibrational spectroscopic imaging and analysis

CIPA invites researchers in Lund and elsewhere to a virtual workshop on spectroscopic techniques and tools, with primary focus on 2D imaging of complex biological/chemical materials.

Infrared, Raman and optical photothermal infrared spectroscopy will be described for researchers curious about using these techniques at facilities in Lund or elsewhere. Challenges of data processing and analysis will be discussed, with examples of suitable methods and software packages. Users of X-ray spectroscopy are also welcome,especially when applications are complementary to vibrational spectroscopy methods.

Participants will be asked to present how they are currently using spectroscopic imaging methods, and/or describe problems which they plan/wish to address with these methods.


September 30 - October 1 2020 | Workshop | Machine Learning for Segmentation of 3D Structures

This online workshop is hosted by the Centre for Quantification of Imaging Data from MAX IV (QIM) and focuses on segmentation of 3D structures in microscopy images using machine learning.


September 16 - 17 2020 | Workshop | Use MATLAB to compare classical image processing techiques with Machine Learning and Deep Learning alternatives - FULLY BOOKED

Do you want to learn how to efficiently and with high precision extract the relevant pictures or shapes out of large data sets? Then you should sign up for the novel workshop on AI and image analysis!

What: Use MATLAB to compare classical image processing techiques with Machine Learning and Deep Learning alternatives
When: Wednesday 16 September, 13-17 and Thursday 17 September 14-17:15
Where: On-line
Registration: CLOSED, workshop is fully booked.

The workshop for 50 participants will be filled on a first come first served basis so do not wait to register. 30 participants are reserved for the Karolinska Insitute but the 20 additional are open for everyone.  Basic knowledge of MATLAB is a prerequisite. If you have any questions, contact Anders Sjöström, CIPA (anders [dot] sjostrom [at] lunarc [dot] lu [dot] se (anders[dot]sjostrom[at]lunarc[dot]lu[dot]se)). Workshop organised by CIPA, KI and the MathWorks.