“Biobank” of functional brain images in the works – A normative database would help future research and diagnostics



Professor Lauri Parkkonen at Aalto University, in collaboration with other researchers, is working towards a “biobank” of functional brain measurements and other digital brain data to enable earlier and better diagnoses of brain disorders. Unfortunately, the current legislation recognises only physical tissue samples for a biobank.

Lauri Parkkonen is a Professor at the Department of Neuroscience and Biomedical Engineering and Director of Aalto Brain Centre, Aalto University. He has worked with brain imaging methods for his whole career. His research focuses on the development of the magnetoencephalography (MEG) methodology and on its application in brain research. The strength of MEG is in its ability to measure brain function at high temporal and good spatial resolution.

“The functioning of the brain, and how it can do what it seemingly effortlessly does, has interested me for so long that I don’t even remember when the interest started,” says Parkkonen.

MEG is a non-invasive medical imaging technique that utilises a set of sensors to detect and record the magnetic fields generated by the electrical activity of the brain. These sensors produce data that can help scientists understand how the brain responds to stimuli such as speech, music, images, and movies.

Moreover, MEG allows scientists to study how the brain develops and changes over time, and how different brain regions are connected and communicate with each other.

One of the most important applications of MEG is in the diagnosis and treatment planning of neurological disorders, such as epilepsy and brain tumours. MEG can identify and locate abnormal brain activity in patients and help doctors determine the best course of surgical treatment.

By providing detailed information about brain activity and connectivity, MEG is paving the way for new discoveries in neuroscience and improving our understanding of brain disorders.

“MEG is a niche in which we are among the best in the world,” Parkkonen says. “Otaniemi has a long tradition in both the development and application of MEG.”

Researchers are developing new clinical applications for MEG. For example, it may be used to map out how tumours change brain function. Unlike any other imaging modality, MEG could also be used to objectively determine the effects of mild head trauma. Another significant clinical application could be in the early diagnosis of progressive memory disorders.

“For example, at the early stages of Alzheimer’s, before clear-cut clinical symptoms, the diagnosis is difficult. Although there is no cure available yet, there are drugs that may slow down the progression of the disease, but these drugs should be given at the early stage of the disease to have an effect,” says Parkkonen.

However, even healthy brains differ from one another, resulting in interindividual variability in MEG recordings. Therefore, these potential clinical applications need a normative database so that MEG signals from a potentially diseased brain can be compared to a statistical model of a healthy brain. Parkkonen and his team have already largely developed a technical solution for this. They have been developing a digital biobank for brain images so that future diagnoses can be more accurate and research more streamlined. Their goal is to create an extensive collection of brain measurements of healthy people of all ages.

Helsinki Brain & Mind has been supporting Parkkonen by supplying his project with ERDF funding and inviting other key stakeholders in the capital region to participate.

As Parkkonen emphasises: “To make this databank succeed, it can’t be done alone. It is a joint effort, and it requires content contributions from many organisations.”

The team has also created a pilot measurement protocol that is ideal for collecting brain measurements for biobanking purposes.

“We needed to determine what stimuli we should present in the measurement to get versatile information about the brain’s functioning without the measurement taking too long,” Parkkonen says.

However, there is a significant obstacle in the way.

The current Finnish biobank law only recognises physical tissue samples, such as blood, and their derivatives as something that can be deposited in a biobank. There are no legal alternatives for reusing brain images.

“The law should be updated,” Parkkonen says. “It doesn’t recognise sole digital samples.”

Parkkonen, his team, and collaborators at HUS have tried to influence the lawmakers to include digital-only samples but revising the law is a long process.

As long as the current law remains unchanged, Parkkonen believes that collaboration with existing biobanks is an option. The large-scale genome project FinnGen that combines multiple biobanks has shown interest in collaborating with Parkkonen.

“By working with existing biobanks, we will be able to select the ideal study population to be invited for MEG measurements,” Parkkonen concludes.

Learn more:
Lauri Parkkonen
Professor at the Department of Neuroscience and Biomedical Engineering, Director of Aalto Brain Centre, Aalto University.
lauri.parkkonen@aalto.fi
+358 40 508 9712

Helsinki Brain & Mind (HB&M) is a regional node of Neurocenter Finland’s national Brain & Mind network.

Helsinki Brain & Mind

Helsinki Brain & Mind promotes high-quality neuroresearch and its utilisation 

The end of 2022 was marked by the official founding of Helsinki Brain & Mind. The network brings together neuroscience researchers from the University of Helsinki, Aalto University and HUS Helsinki University Hospital to advance interdisciplinary collaboration, research, and innovation. Now that the official papers have been signed, it is a good time to look back on how the network came to be what it is today.

Read more

Selvityksestä apua henkilötietojen käsittelyyn tutkimuksessa 

Selvitys: Henkilötietojen käsittely tutkimuksessa – Helsinki Brain & Mind (helsinkibrainandmind.fi)

Työkalu: Tutkimusdatan sisältö ja vaaditut toimenpiteet

Nykyinen lainsäädäntö koskien henkilötietojen käyttöä tutkimuksessa nähdään monimutkaisena ja tulkinnanvaraisena. Tuoreessa selvityksessä kartoitetaan terveyttä koskevien henkilötietojen tutkimuskäyttöä koskevaa lainsäädäntöä ja tulkintoja sekä annetaan ohjeita tutkijoille parhaista toimintatavoista. 

Usein tutkija ei ota huomioon henkilötietosuostumusta pyytäessään, että tiedoille saattaa olla tarvetta myös jatkotutkimuksessa. Tämä johtaa siihen, että tutkittavilta joudutaan jälleen pyytämään suostumusta, mikä mutkistaa uuden tutkimuksen aloittamista. 

Tämä on harmillinen tilanne, mutta ei harvinainen sellainen. 

Henkilötietojen käsittely tutkimuksessa on hankala kokonaisuus, josta selviytyminen on työlästä tutkijoille ja jopa juristeille. Hämmennystä aiheuttaa varsinkin se, että tapauksien tulkinnat saattavat olla erilaiset riippuen organisaatiosta. Alusta asti on otettava huomioon monia yksityiskohtia, joista tutkijan on vaikea pysyä kärryillä ja jotka harvoin kiinnostavat häntä. 

Ongelmaa selvitettiin Helsinki Brain & Mindin Digitalisaatiolla aivoterveyttä -hankkeessa. Selvityksestä vastaava Iiris Malinen teki sen selventääkseen henkilötietojen tutkimuskäytön juridiikkaa asiasta kiinnostuneille. Selvitys sisältää myös erillisiä kohtia, jotka on tarkoitettu käytännölliseksi avuksi tutkijoille (kohdissa 4, 5, 8 & 9). 

“Tutkijaa voi erityisesti kiinnostaa selvityksen prosessikuvaukset ja check-listit”, Malinen kertoo. 

Selvityksessä avataan oleellisia käsitteitä ja selvennetään, millaisia toimintatapoja tulisi noudattaa henkilötietojen käsittelyn suhteen lääketieteellisessä ja ei-lääketieteellisessä tutkimuksessa. Prosessia kirkastetaan käytännönläheisin kuvauksin ja tarkistuslistoin. 

Selvitys julkaistaan HB&M-sivuilla, ja sitä tullaan päivittämään lainsäädännön muuttuessa. Lisäksi siitä ollaan kehittämässä graafista päätöksentekopuuta, joka auttaa nopeasti hahmottamaan omaan tutkimukseen tarvittavaa prosessia. 

Henkilötietojen käytölle toivotaan selkeämpää ohjeistusta 

Selvityksen laatimisen yhteydessä keskusteltiin Helsingin yliopiston, Aalto-yliopiston ja HUSin tutkijoiden ja juristien kanssa. Keskusteluissa nousi esiin, mitkä tilanteet aiheuttavat haasteita ja vaatisivat selkiyttämistä. 

Milloin lain silmissä täyttyy lääketieteellisen tutkimuksen määritelmä? Entä onko jatkotutkimus henkilötiedoilla mahdollista? 

Yhteisenä toiveena oli paitsi lainsäädännön kartoittaminen, myös käytännönläheisten ohjeiden laatiminen, jotta hankalaa kokonaisuutta olisi helpompi hallita. 

Eettiset kysymykset ovat aina monitulkintaisia 

Keskustelua käytiin myös kolmen eri tutkimuseettisen toimikunnan kanssa. Yhtenäisiä linjoja päätöksenteolle ei vaikuta kaikilta osin olevan. Tämä voi johtua paitsi erilaisista lain ja tutkimusetiikan tulkinnoista, myös siitä, että jokaista eettisen toimikunnan käsittelemää tutkimusta arvioidaan tapauskohtaisesti. Projektin kokonaisuudesta ja sen elementeistä riippuu, millainen päätös tehdään. 

Tutkimuseettisten toimikuntien lausunnot eivät ole julkisia, mikä voi osittain selittää yhtenäisen linjan puutetta. 

“Selvitys voi auttaa luomaan keskustelua siitä, kuinka eroavia käytännöt voivat joissain tilanteissa olla. Tämä voi johtaa käytäntöjen lähenemiseen”, Malinen sanoo. 

Tutkijoita voidaan tukea 

Vaikka henkilötietojen käyttäminen tutkimuksessa voi tuntua sumalta, tutkijan on mahdollista saada prosessiin apua. 

Malinen toivoo, että tutkijat uskaltavat hakea apua varhain. Apua on saatavilla yliopistojen tukipalveluista, kuten lakipalveluista. Tärkeintä on tietää, mistä apua saa ja mihin sitä tarkalleen tarvitaan. 

Selvityksen tukena julkaistava työkalu auttaa tutkijaa hahmottamaan, mitä vaiheita oman tutkimuksen toteuttamiseen kuuluu. Kun lähtökohta selkenee, on helpompi paikantaa, missä asioissa on vielä epäselvyyttä. 

Selvitys toteutettiin osana Helsinki Brain & Mind -verkoston Digitalisaatiolla aivoterveyttä -hanketta. Hankkeella pyritään edistämään aivoterveyttä uusin teknologisin ratkaisuin ja innovaatioin. Näin luodaan mahdollisuuksia tutkimukselle, hyvinvoinnille ja yrityksille sekä saadaan Uusimaasta kilpailukykyinen aivoterveyttä edistävien ratkaisujen keskus. 

Selvitys on luettavissa Helsinki Brain & Mindin sivuilla.  

Selvitys: Henkilötietojen käsittely tutkimuksessa – Helsinki Brain & Mind (helsinkibrainandmind.fi)

Työkalu: Tutkimusdatan sisältö ja vaaditut toimenpiteet

MAGICS makes high-tech tools available for common use 

The virtualization technologies that researchers need are now easily accessible through the MAGICS consortium. This collaboration between universities makes it possible to use cutting-edge technology to research immersive and naturalistic remote presence among many other things. With cooperation and the right equipment, research can cross scientific boundaries. 

Person wearing a portable MoCap suit in motion capture studio

The motion capture studio and portable MoCap suit can be used to record the user’s movements.
Photo: Aalto University. 

What if you could measure how a hall full of people simultaneously reacts to an opera? Or maybe you could create just the situation needed to study human behavior and easily customize it according to the results. Imagine being able to analyze an interaction, pause it, and view it from multiple points of view. All this and more is possible with the help of the MAGICS consortium.

Aalto University, Tampere University, and University of Arts Helsinki (Uniarts) have teamed up to create a network of infrastructures to advance science towards new directions. Cutting-edge technologies have been selected according to the interests of researchers and divided between these universities to encourage and inspire interdisciplinary research that crosses scientific boundaries.

“With the MAGICS infrastructure you can take a step outside laboratory environments into more natural conditions,” says Mikko Sams, Professor of Cognitive Technology at Aalto University and Academic leader of MAGICS. 

The base ideology of MAGICS is in proactivity and a curiosity-driven approach to science. Researchers can use any technology from the MAGICS locations. People are encouraged to experiment with the available technology and see how it can benefit their research. The MAGICS community has experts who know how the technology works and who can give insights on how it can be used for different purposes. 

“We listen to what people need and give them innovative suggestions on how they could use MAGICS technology to achieve their goals,” says Roope Raisamo, Professor in Human-Technology Interaction at Tampere University. 

MAGICS also supports researchers in describing the technologies in funding applications if needed. 

Several successful use-cases

The MAGICS infrastructure is already in active use. Upwards of 20 research groups are regularly using the infrastructure. For example, researchers are studying the effects of VR on therapy and measuring how people react – how they move, what their eyes focus on, and what is happening in their brains. Applications in clinical research are also being tested in collaboration with HUS. In Tampere, MAGICS equipment has been used in collaboration with Tampere University Hospital to develop new methods for diagnosis and surgery planning using medical imaging data and virtual reality technologies. Another use case is new methods to support collaboration in shared virtual reality environments. 

Person testing virtual reality equipments.

Olfaction technology can be used to smell objects in virtual reality, like the apple pictured.
Photo: Tampere University/TAUCHI, Päivi Majaranta

MAGICS also has great potential for education. “By bringing such technology to students and staff they come to understand the phenomenon and its uses, which makes way for new ideas,” says Tero Heikkinen, university researcher at Uniarts. 

Scientists are not the only ones who benefit from MAGICS. There has also already been collaboration between MAGICS and companies from different industries to use the technology for more commercial development projects.  

One year to find all necessary infrastructure 

The project got its funding of 2,4 million euros from Academy of Finland in 2020 with the caveat that all the money was to be used within a year. After discussions with multiple researchers, the equipment in the MAGICS infrastructure was chosen according to their needs. Now the consortium is in full swing, and the tools are available for easy use. 

“We also want to build a MAGICS community that meets to discuss common interests, generates new ideas, and forms multidisciplinary research groups of experts to tackle difficult problems,” Sams describes. “This process is still on its way, but we are off to a good start.” 

Expanding the network and working on shared projects 

The plan is to increase collaboration between other universities so that the network can be beneficial for researchers and companies throughout Finland.  

Computer and big screen in Visualization Hub.

A team can experience and design 360° environments,
like games or architecture, in the Visualization Hub.
Photo: Aalto University

“The opening of the brand new Marsio building at the Aalto campus will be in the early autumn of 2024. Among other things, it will contain a media center and spaces for various events. It will offer possibilities where researchers can gather data from individuals and groups of different sizes,” says Antti Ruotoistenmäki, the academic coordinator of MAGICS Aalto.   

MAGICS will continue to keep the infrastructure and technologies up to date. Next up: concrete collaboration projects that connect researchers in different universities. 

Find out more about MAGICS and keep up with upcoming events through their website. 

Carita Salminen, Helsinki Brain & Mind

Neurocenter Finland and the nationwide Brain & Mind network support multidisciplinary neuroscientific research, development, and further cooperation between universities, hospitals, and businesses. MAGICS has a similar mission, which is why this story is published by Helsinki Brain & Mind. 

 Helsinki Brain & Mind neuroscience network represents the University of Helsinki, Aalto-University, and HUS Helsinki University Hospital.  
Tampere Brain & Mind neuroscience network represents Tampere University and Tampere University Hospital. 

They are regional nodes of Neurocenter Finland’s Brain & Mind network.  

Subscribe to the Helsinki Brain & Mind newsletter!
More Helsinki Brain & Mind News

Researchers’ Corner: Anna-Elina Lehesjoki

“My research aims at a better understanding of the molecular genetic basis of rare epilepsy syndromes with identification of the underlying defective genes as a starting point.”

Anna-Elina Lehesjoki
Research Director, Folkhälsan Research Center
Professor, Medicum, University of Helsinki

What are your research topics?

My research aims at a better understanding of the molecular genetic basis of rare epilepsy syndromes with identification of the underlying defective genes as a starting point. This enables establishment of molecular genetic diagnostics for these diseases. In the long term, the research contributes to development of novel therapies for epilepsy.

Our current focus in gene identification is on the rare group of progressive diseases with myoclonus and epilepsy as the major clinical manifestations, the PMEs. We employ genome-wide approaches, i.e. exome and genome sequencing to identify the underlying genes. Our recent work suggests that PMEs have highly heterogeneous genetic etiologies encoding gene involved in a variety of cellular processes. The work is done in international collaboration, the consortium co-headed by me and Prof. Sam Berkovic in Melbourne.

A central focus of research in my team deals with investigation of disease mechanisms underlying the most common PME disease, EPM1, which is caused by partial loss-of-function mutations in the gene encoding cystatin B, a cysteine protease inhibitor. We are utilizing cystatin B -deficient (Cstb-/-) mice and patient-derived induced pluripotent stem cells (iPSC) as models and are applying various omics approaches in our research. We have shown the central contribution of early microglial activation and dysfunction in the disease pathogenesis in Cstb-/-mice, and deciphering the molecular mechanisms associated with microglial dysfunction in EPM1 is an important focus of our research today.

Based on your research, what is (are) the most central, most urgent, or most exciting unresolved question(s) in the epilepsy field?

Molecular genetic studies during the past two decades have unraveled an unprecedented etiological heterogeneity in epilepsy. This concerns both the rare epilepsy syndromes and the common genetic epilepsies with a polygenic and multifactorial etiology. The vast heterogeneity poses challenges for the development and implementation of personalized therapies for genetic epilepsies. Indeed, despite advances in understanding underlying genetic etiologies and disease mechanisms, medical treatment of epilepsy today rarely targets the underlying disease process.

Given the number of identified genes and variants, many with different functional outcomes even within single genes, developing precision therapies for genetic epilepsies is the most urgent, and most challenging task for the epilepsy research community. To achieve this, close collaboration between clinical and translational researchers is essential to identify the most critical needs for targeted therapies. Better functional understanding is needed to enable targeting therapies for functionally similar variants as a group rather than each individual variant separately. Robust preclinical models combined with novel function tools are a prerequisite for success in developing precision therapies for epilepsy. Finally, the epilepsy community needs to prepare for upcoming clinical trials with the precision treatments.

Regarding my own research the most critical question is to understand how partial loss of cystatin B function increases neuronal excitability and impairs neuronal survival during the life of EPM1 patients, resulting in progressive, highly treatment-resistant, and severely disabling myoclonus with cognition being largely preserved. This mechanistic understanding is needed for development of precision therapies for EPM1 patients, primarily for treatment of the disabling myoclonus.

Back to Researchers’ Corner
Subscribe to the Helsinki Brain & Mind newsletter!