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News

Spectroscopic data processing and analysis webinar

On 15th February 2023, Carl Troein, CIPA Application Expert specialised in 2D spectroscopy analysis, held the webinar “Spectroscopic Data Processing and Analysis” on behalf of CIPA – the coordinating unit of the InfraVis Lund node. The webinar covered problems in spectroscopic data analysis and methods for their identification and correction as well as for analysis and visualization. Examples included 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 as well as mage analysis and classification. 

Researchers from eight different Swedish universities and international organisations attended the webinar, and those who had brought their data with them received free consultations from Carl Troein, where Carl examined the data and made suggestions for corrections and improvements. 

If you missed out on the webinar, we will make the recording available shortly, and if you would like a consultation data handling and data analysis, feel free to contact CIPA director Kajsa M Paulsson at kajsa_m [dot] paulsson [at] med [dot] lu [dot] se (kajsa_m[dot]paulsson[at]med[dot]lu[dot]se).


LUNARC replaces its High-Performance Computing cluster 

LUNARC - the center for scientific and technical computing at Lund University is a highly relevant resource for the CIPA community. LUNARC is replacing the Aurora cluster which has been in operation for the last six years. The replacement resource COSMOS is now being installed and will be made available to researchers in March 2023. COSMOS represents a significant increase in computational capacity and will offer access to modern hardware including GPUs. Through the LUNARC Desktop, new and existing users will be able to draw upon the benefits of high-performance computing (HPC) without having to be burdened by the intricacies of HPC utilisation. At the same time, users proficient in HPC usage will still be able to make use of the computational power represented in the interconnected nodes of COSMOS.

A part of COSMOS

Renewed and increased Faculty of Science research infrastructure grant to CIPA

On the 11th of November 2022, CIPA received renewed support from the Faculty of Science at Lund University. The motivation behind the decision to grant CIPA 800 000 SEK was that CIPA has, more and more evidently, established itself as an important research infrastructure needed for handling imaging data. The need for technical support in image processing and analysis is expected to continue to grow at Lund University, in step with the expected increase in the imaging data generated at different infrastructures, including the Microscopy Facility at the Department of Biology (M-Bio). The grant ensures continued access to the competence of Carl Troein, specialized in microspectroscopy - one of the six CIPA application experts.

- Carl, what kind of users can you help and how?

I have a broad background in developing analysis and data processing methods for biological data. Since my main focus at CIPA is on 2D spectroscopic imaging data, I can help users with spatially resolved FTIR, Raman, O-PTIR and hyperspectral IR imaging, but I am happy to discuss other types of data as well. My software expertise is mainly in Python and C++ programming, combining and developing steps such as data pre-processing, dimensionality reduction, machine learning classification and generating figures. I can implement pre-existing methods, file formats and other tools in open-source software (e.g. Orange/Quasar), but also develop new algorithms for, for example, processing new types of data or solving specific problems. 

The above-listed methods have various advantages and applications. FTIR can quickly acquire images of tissues and other structures at resolutions down to 2-3 µm; O-PTIR (optical photothermal infrared) probes infrared absorption at 500 nm resolution, at the expense of time and spectral range; Raman brings out other information [MOU2] than infrared absorption spectra; Hyperspectral imaging can produce images of larger areas at shorter wavelengths. Considering the range of these methods, they can, for example, be used to help users detect and quantify differences in chemical composition, locate lipids in tissues and distinguish between cell types.

Considering the successful establishment of the Microscopy Facility at the Department of Biology (M-Bio) where competencies offered by Carl Troein and by CIPA at large can be particularly useful, we spoke with Ola Gustafsson - research engineer at M-Bio and Marie Dacke - Professor of Sensory Biology.

- How would you describe the need for technical support with handling imaging data at the Microscopy Facility at the Department of Biology (M-Bio)?

The users of the Microscopy Facility at the Department of Biology (M-Bio) will require both basic and more advanced technical support with handling imaging data. Primarily, we hope that CIPA will be able to support us with image analysis, processing and visualisation of the large data sets that will be generated when the new micro CT equipment is installed at the department. Apart from basic visualisation support, we will need CIPA’s help with more complex quantitative data extraction in the future. Support with confocal and electron microscopy data might also be requested. 

- How do you envision the development of a collaboration between CIPA and the M-Bio?

We envision our users connecting with the CIPA experts much more frequently in the future as well as CIPA experts giving our users input on different needs prior to data acquisition. To make this happen, a tighter cooperation between us and CIPA will need to be established.

Carl Troein. Portrait photo.
Carl Troein. CIPA Application expert, microspectroscopy.

Do you need access to hardware or software for image analysis and processing? Or do you need advice and support from one of the six CIPA application experts? CIPA provides support for researchers from all faculties at Lund University, including the Faculty of Medicine. Learn more about the expertise available at CIPA here.


InfraVis Meeting Days in Uppsala

On the 5th and 6th of September, 2022, Uppsala University Node Coordinator Ingela Nyström, together with her team, hosted the InfraVis Meeting Days. The InfraVis team, with representatives from nine partner universities, gathered to review the progress made by the Research Infrastructure, to brainstorm paths for future development, and to network.  

The Lund University node was well-represented: Lund University Node Coordinator Anders Sjöström, National Technical Coordinator Kajsa M Paulsson, InfraVis Communications Lead Katja Woxell, Steering Committee member Melvyn B Davies and InfraVis application experts Mattias Wallergård, Günter Alce, Henrik Garde and Jonas Ahlstedt were all present.

InfraVis Meeting Days

Jonas Ahlstedt held a workshop "From modelmaking to raytracing" where the InfraVis team got to work in pairs on simple 3D animations by the help of Blender. Considering the fact that not every InfraVis member is an animation expert, this workshop was a fun and educational team-building exercise. Anders Sjöström presented the progress of the Lund University pilot projects, and Katja Woxell presented the InfraVis Communication Strategy at the Steering Committee meeting.

Click here to read more about the InfraVis Meeting Days.


New regulations on fees for the use of research infrastructures

The government has introduced a new regulation regarding the fees that state universities may charge external actors for using the university research infrastructures, for example, databases, laboratories or large-scale computing tools. The aim is to support Swedish universities in making their research infrastructures accessible.

Swedish universities already charge fees for using their respective research infrastructures, but the new regulation allows them to charge fees for all parts of the research infrastructures, including costs for personnel and peripheral materials needed for using the research infrastructure.


CIPA Kickoff 2022

With a team-building and fun first day of the term, CIPA team is officially back in business!

The team spent a day defining the direction of CIPA for the fall term, including CIPA events, user support and cross-border collaborations, to name just a few. CIPA is about to embark on an even more exciting journey. If you haven't yet, come on board!

CIPA Team at CIPA Kickoff 2022
The 2022 CIPA team