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Kajsa M Paulsson, Head of unit

Kajsa M Paulsson

CIPA was initiated and is headed by Kajsa M Paulsson. While leading her research group at Experimental Medical Science, Kajsa has in parallel built a reputation and competence in management of Research Infrastructures. She has, for example, been a board member of a number of Swedish and European Research Infrastructures and initiatives. She is also an acknowledged evaluator of Research Infrastructures and has developed organizational models for different types of Research Infrastructures. Having graduated from her Executive Masters in Business Administration (EMBA) focused on Research Infrastructures, Kajsa has a unique tool box for Research Infrastructure work including legal, financial, strategic and organizational issues, each of which are equally important for the development of CIPA.

Contact: kajsa_m [dot] paulsson [at] med [dot] lu [dot] se

Anders Sjöström, CIPA coordinator, processing and HPC expert, LTH

Anders Sjöström

Anders studied computer science and mathematics at Lund University. Since then Anders has been working as a research engineer at Lund university as well as an application expert in HPC at LUNARC. Anders is an expert in using MATLAB on large computer resources and has twenty years of experience in using supercomputer resources.

Contact: anders [dot] sjostrom [at] construction [dot] lth [dot] se

Katja Woxell, Communications Officer

Katja Woxell. Communications Officer

Katja holds a master’s degree in Language and Linguistics and is specialized in Cognitive Semiotics – the transdisciplinary science of language, communication, media and mind. She has a background as a copywriter, journalist and scientific editor as well as ten years of experience as a language teacher and translator, all of which have helped her build skills that come in handy in different ways in her work as a communications officer. She is an aspiring researcher with focus on empathy and movement. Katja considers her strong interest in research her primary advantage as Communications Officer for the research infrastructures CIPA and InfraVis.

Contact: katja [dot] woxell [at] med [dot] lu [dot] se 

CIPA Application Experts

Carl Troein, 2D Spectroscopy analysis expert, FoS

Carl Troein, CIPA application expert, spectroscopy.

Background: Developing analysis and data processing methods for biological data.   

Uses the following methods:  
-Spatially resolved FTIR: Quickly acquires images of tissues and other structures at resolutions down to 2-3 µm;   
-Raman: brings out information other than infrared absorption spectra;  
-O-PTIR (optical photothermal infrared): Probes infrared absorption at 500 nm resolution, at the expense of time and spectral range; 
-Hyperspectral IR imaging: Produces images of larger areas at shorter wavelengths.  

Applications involved in: Combining and developing steps such as data pre-processing, dimensionality reduction, machine learning classification and generating figures. 

Programming languages: Mainly in Python and C++ programming  

Contact: carl [at] thep [dot] lu [dot] se

Alexandros Sopasakis, Expert in machine learning applications, LTH

Alexandros sitting infront of a book shelf. Photography.

Background: Mathematics, stochastic microscopic systems and their interactions. Simulations with Monte Carlo methods - numerical analysis.

Uses the following Machine Learning methods (selection):  
LSTMs, TCN, Decision Trees: for time series analysis;  
UNets, ResNets, Mask-RCNN, Fast-RCNN, Faster-RCNN: for classification/segmentation; 
SIM-CLR, VAEs, GANs: for data generation and anomaly detection. 

These methods/competencies/applications can be used for:  
- Running massive data requiring both large processor memory or fast parallel processors; 
- Forecasting from spatial/temporal or other data; 
- instance segmentation and area or volume estimation of bacteria/cells/glomeruli among others;
- super-resolution. 

Applications involved in (selection): general image analysis from video/images; MRI instance segmentation & volume computation; time series analysis; feature importance; anomaly detection; data generation; point-clouds; Sentinel-1,2,3 & Copernicus satellite data downloading, cleaning, despecling and analysis. 

Programming languages (selection): C, C++, Python, Matlab, Mathematica.  
Supercomputer systems experience: Alvis, Google Colab, AWS (limited). 

Contact: alexandros [dot] sopasakis [at] math [dot] lth [dot] se

Jonas Ahlstedt, Image analysis and visualization expert, FoM

Jonas Ahlstedt

Jonas studied medical radiation physics as a grad student before pursuing a PhD in medicine. Working at CIPA as well as at Lund University Bioimaging Centre (LBIC), Jonas focuses mainly on supporting users with image analysis in the field of life sciences.

Contact: jonas [dot] ahlstedt [at] med [dot] lu [dot] se

Emanuel Larsson,Tomographic image analysis expert, LTH

Emmanuel Larsson, photo. Photographer: private

Emanuel studied Engineering Biology at Linköping University, and later on obtained a Joint PhD in Molecular Physics and Information Engineering from Linköping University and University of Trieste, Italy. He has previously been stationed at both micro and nano tomography beamlines at Synchrotron facilities. Emanuel mainly focuses on supporting users with tomographic X-ray and neutron imaging and image analysis, within CIPA, QIM - Center for Quantification of Imaging Data from MAX IV, and the ForMAX portal, at LUNARC and at the Division of Solids Mechanics.

Contact: emanuel [dot] larsson [at] solid [dot] lth [dot] se 

Previous Application Experts

Emil Tykesson, CryoEM data analysis expert, FoM

Emil Tykesson. Photo
Emil Tykesson. Photo

Emil is an organic chemist by training. He has studied a range of human carbohydrate (glycosaminoglycan)-modifing enzymes and his work has covered many aspects of structural biology and enzyme/carbohydrate characterization. In 2020, his team solved the first structure of the human carbohydrate-modifing enzyme dermatan sulfate epimerase 1, known to be upregulated in many types of cancer. Together with his collaborators, he is currently trying to design small molecule inhibitors of the enzyme.

Since 2021, Emil has been employed as a cryo-EM expert, supporting the life science user community in Lund with sample preparation and data analysis, involving a lot of work with SNIC high-performance computing resources.

Contact: emil [dot] tykesson [at] med [dot] lu [dot] se