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Our Goal

... is to utilize the neural circuits of the retina to reveal fundamental principles of neural computations at quantal resolution.

Research Overview

Our ability to see in vastly varying conditions depends critically on the outstanding performance of vision. Vision begins in the neural circuits of the retina, which operates with a remarkable fidelity. We study novel signal processing mechanisms and their adaptive dynamics at the synaptic and cellular-element level across the entire neural circuit of the retina.We do so by combining a battery of techniques allowing precise manipulations of local signal and noise statistics in a well-defined retinal circuit relying on genetically modified mice, molecularly tailored artificial visual pigment molecules, and cutting-edge electrophysiological recording techniques. We seek to understand the functional implications of novel retinal signal processing mechanisms by correlating our results with the output of the entire visual system measured in mouse behavioral experiments and human psychophysics experiments.

Programming project in visual neuroscience:
Mobile solution for managing video recordings, real-time tracking and data management of behavioral experiments on freely-moving mice

Project description

We are seeking a highly-motivated software developer with a keen interest in web technologies. Our lab continuously strives to develop novel approaches in the field of behavioral neuroscience and part of this includes development of solutions for supervision and automated data management during animal experiments. The goal of this project is to finalize a web based system used during behavioral experiments on mice, through which the experimenter can control the experiment and simultaneously record and store videos and metadata.

Current system specs:
  • Backend: Docker, Django, PostgreSQL, REST
  • Frontend: Docker, Vue.js, NodeJS, Nginx
Prerequisites:
  • The applicant is expected to be interested in web development and to handle standard tools such as git, docker and nginx web server.

The project could constitute a summer job or form the basis for a master thesis.
If you are interested, please contact: Johan Westö (johan.westo@aalto.fi, +358 44 358 4836)

Working environment

The Ala-Laurila lab aims to break new frontiers by revealing fundamental principles of how visual information is encoded in the retina and how the brain reads this neural code to drive animal behavior. Research methods in the lab include cutting-edge optical imaging, electrophysiological recording techniques, precise manipulations of retinal circuit function, mathematical modelling and state-of-the-art and beyond behavioural assays to reach these goals.

For more see:
Akatemiapalkinto 2014 Petri Ala-Laurila
Suomalaiset aivotutkijat kumosivat vanhan peruskäsityksen hermoston toiminnasta (Helsingin sanomat)
Näön rajoilla (Helsingin sanomat, Teema)

Publications


Westo, J. & Ala-Laurila, P. (2020). Seeing beyond violet: UV-cones guide high-resolution prey-capture behavior in fish. Neuron 107, 207-209.
[ PDF ]

Koskela, S., Turunen, T. & Ala-Laurila, P. (2020). Mice reach higher visual sensitivity at night by using a more efficient behavioral strategy. Current Biology 30, 1–12.
[ PDF | COMMENTARY | FACULTY OF 1000 | PRESS RELEASE ]

Smeds, L., Takeshita, D., Turunen, T., Tiihonen, J., Westö, J., Martyniuk, N., Seppänen A. & Ala-Laurila, P. (2019). Paradoxical Rules of Spike Train Decoding Revealed at the Sensitivity Limit of Vision. Neuron 104, 1–12.
[ PDF | COMMENTARY | PRESS RELEASE ]

Tikidji-Hamburyan, A., Reinhard, K., Storchi, R., Dietter, J., Seitter, H., Davis, K.E., Idrees, S., Mutter, M., Walmsley, L, Bedford, R.A., Ueffing, M, Ala-Laurila, P., Brown,T.M., Lucas, R.J. & Münch , T.A. (2017). Rods progressively escape saturation to drive visual responses in daylight conditions. Nature Communications 8.
[ PDF | FACULTY OF 1000 ]

Takeshita, D., Smeds, L. & Ala-Laurila, P. (2017). Processing of single-photon responses in the mammalian On and Off retinal pathways at the sensitivity limit of vision. Phil. Trans. R. Soc. B 372.
[ PDF ]

Ala-Laurila, P. (2016). Visual Neuroscience: How Do Moths See to Fly at Night? Current Biology 26, R229–R246.
[ PDF ]

Vartanian, G.V., Li, B.Y., Chervenak, A.P., Walch O.J., Pack W., Ala-Laurila, P. & Wong K.Y. (2015). Melatonin Suppression by Light in Humans Is More Sensitive Than Previously Reported. J Biol Rhythms 30, 351-354.
[ PDF ]

Ala-Laurila, P. & Rieke, F (2014). Coincidence Detection of Single-Photon Responses in the Inner Retina at the Sensitivity Limit of Vision. Current Biology 24, 2888-2898.
[ PDF | COMMENTARY ]

Ala-Laurila, P., Greschner, M., Chichilnisky & Rieke, F (2011). Cone photoreceptor contributions to noise and correlations in the retinal output. Nature Neuroscience 14, 1309-1316.
[ PDF ]

Ala-Laurila, P., Cornwall, M.C., Crouch, R.K., & Kono, M. (2009). The action of 11-cisretinol on cone opsins and intact cone photoreceptors. J Biol Chem 284, 16492-16500.
[ PDF ]

Estevez, M.E., Kolesnikov, A.V., Ala-Laurila, P., Crouch, R.K., Govardovskii, V.I., & Cornwall, M.C. (2009). The 9-methyl group of retinal is essential for rapid Meta II decay and phototransduction quenching in red cones. J Gen Physiol 134, 137-150.
[ PDF ]

Ala-Laurila, P., Donner, K., Crouch, R.K., & Cornwall, M.C. (2007). Chromophore Switch from 11-cis-dehydroretinal (A2) to 11-cis-retinal (A1) Decreases Dark Noise in Salamander Red Rods. J Physiol 585, 57-74.
[ PDF ]

Cornwall M.C., & Ala-Laurila P. (2007). A perfect marriage: molecular genetics ties the knot with electrophysiology in studies of visual transduction. J Gen Physiol 130, 7-10.
[ PDF ]

Jokela-Määttä, M., Smura, T., Aaltonen, A., Ala-Laurila, P., & Donner, K. (2006). Visual pigments of Baltic Sea fishes of marine and limnic origin. Vis Neurosci 24, 389-398.
[ PDF ]

Kolesnikov, A.V., Ala-Laurila, P., Shukolyukov, S.A., Crouch, R.K., Wiggert, B., Estevez, M.E., Govardovskii, V.I., & Cornwall, M.C. (2006). Visual cycle and its metabolic support in gecko photoreceptors. Vision Res 47, 363-374.
[ PDF ]

Estevez, M.E., Ala-Laurila, P., Crouch, R.K., & Cornwall, M.C. (2006). Turning Cones Off: The Role of the 9-Methyl Group of Retinal in Red Cones. J Gen Physiol 128, 671-685.
[ PDF ]

Pahlberg, J., Lindström, M., Ala-Laurila, P., Fyhrquist-Vanni, N., Koskelainen, A., & Donner, K. (2005). The photoactivation energy of the visual pigment in two spectrally different populations of Mysis relicta (Crustacea, Mysida). J Comp Physiol A Neuroethol Sens Neural Behav Physiol 191, 837-844.
[ PDF ]

Ala-Laurila, P., Donner, K., & Koskelainen, A. (2004). Thermal activation and photoactivation of visual pigments. Biophys J 86, 3653-3662.
[ PDF ]

Ala-Laurila, P., Pahlberg, J., Koskelainen, A., & Donner, K. (2004). On the relation between the photoactivation energy and the absorbance spectrum of visual pigments. Vision Res 44, 2153-2158.
[ PDF ]

Tsina, E., Chen, C., Koutalos, Y., Ala-Laurila, P., Tsacopoulos, M., Wiggert, B., Crouch, R.K., & Cornwall, M.C. (2004). Physiological and microfluorometric studies of reduction and clearance of retinal in bleached rod photoreceptors. J Gen Physiol 124, 429-443.
[ PDF ]

Ala-Laurila, P., Albert, R.-J., Saarinen, P., Koskelainen, A., & Donner, K. (2003). The thermal contribution to photoactivation in A2 visual pigments studied by temperature effects on spectral properties. Vis Neurosci 20, 411-419.
[ PDF ]

Ala-Laurila, P., Saarinen, P., Albert, R., Koskelainen, A., & Donner, K. (2002). Temperature effects on spectral properties of red and green rods in toad retina. Vis Neurosci 19, 781-792.
[ PDF ]

Koskelainen, A., Ala-Laurila, P., Fyhrquist, N., & Donner, K. (2000): Measurement of thermal contribution to photoreceptor sensitivity. Nature 403, 220-223.
[ PDF | COMMENTARY ]

Ala Laurila's team

Members

Click image for description

Petri Ala-Laurila, DSc (Tech)

Associate professor

I am a “kid” who loves science. I did my PhD in Finland (2000- 2003, Engineering Physics, Helsinki University of Technology) and thereafter moved to the USA, where I did two distinct postdoctoral periods: in Boston (2004-2008, laboratory of Dr. Carter Cornwall) and in Seattle (2008-2012, laboratory of Dr. Fred Rieke). The goal of my lab is to establish a new frontier in the Finnish neuroscience community focusing on signal processing in the mammalian retina.

Gabriel Peinado, PhD

Postdoctoral Fellow

I want to understand how sensory systems filter and sample information to create the reality that each of us subjects inhabits. I started my career studying how isolated photoreceptors respond to light stimuli. For my Ph.D. I then investigated how photoreceptor cells, Müller cells and the Retinal Pigment Epithelium function together to mediate vision in the living eye. I am now excited to participate in understanding how the information acquired by photoreceptors is encoded by neural circuits underlying visual perception!

Johan Westö, PhD

Postdoctoral Fellow

I'm an eager learner and a voracious reader who is interested in a lot of things. The act of learning itself is, nonetheless, something that stands out and which has fascinated me throughout my life. This is as true today as ever before, and it has fuelled my curiosity for understanding learning in brains as well as in machines. Understanding how an agent (brain or machine) learns to make sense of its surrounding is in my opinion the ultimate quest in life.

Krishna Dovzhik, MSc

PhD Candidate

I'm a Marie-Curie fellow exploring the interface between neuroscience and physics with a deep interest in fundamental topics and their connection to new potential applications. My formative years I spent in Anton Zeilinger's group in Vienna doing research in quantum physics, from basic questions to quantum technologies and their use in diverse fields, including biology. Among my other interests, vision has a special role. Revealing the interdisciplinary links and creating new methods for vision research are my goals here.

Nataliia Martyniuk, MSc

PhD Candidate

I believe that vision is the most important human sense, because it often gives the most immediate impression of the world. Visual perceptions arise in the neural circuits of the retina, which detect and encode the visual information and transmit it to the brain, which forms the basis for our decisions. I'm highly impressed with the technical capabilities and the level of innovation in the laboratory of Professor Petri Ala-Laurila and I am looking forward to be part of such a motivated and talented team.

For more information about my PhD program please visit the website:
http://www.uef.fi/web/biomep/doctoral-students

Aleksandra Poluianova, MD

PhD Candidate

I hold a degree of Doctor of Medicine (2013-2019) from Sechenov University (the Russian Federation). Without a doubt, visual perception is considered the most crucial ability which helps human interact with the outside world. Unfortunately, there is a large number of conditions that are associated with impaired transmission due to damage of the retina. The Ala-Laurila Lab provides an opportunity to study signaling processes and behavior, which will subsequently give us the possibility to determine the pathogenesis of the disease and its solutions.

Aarni Seppänen, MSc (Tech)

PhD Candidate

My passion for neuroscience stems from one of the most fundamental questions: How does the brain work? Surprisingly, this question can be approached by studying signal processing in the retina. In my opinion, the Ala-Laurila lab is working on the most important topics in neuroscience by bridging the gap between the function of neural circuits and behavior. I am grateful for being able to work with the great people in this lab and I try to live by the wise words of Fernando Pessoa: “Put all you are into the smallest thing you do”.

Lina Smeds, MSc

PhD Candidate

I grew up in the small town of Porvoo, Finland. In 2009 I moved to Helsinki where I started to study biology with physiology and neuroscience as my major. I was happy to join the lab in June 2012 and started conducting behavioral experiments on mice. I enjoy challenges, and a need to learn and discover new things drives me to do research. My favorite motto that goes for my attitude towards both science and life in general is: "Don’t be pushed by your problems. Be led by your dreams."

Jussi Tiihonen, MSc (Tech)

PhD Candidate

I'm a Master's student at Aalto University with a major in Life Science Technologies. Research and scientific methods have interested me as long as I can remember. I'm glad to be able to do research while studying for the future.

Tuomas Turunen, MSc (Tech)

PhD Candidate

In 2012, I recieved my Master's degree in computer science from Aalto University. The focus of my degree was on computer vision and object recognition. Out of pure interest after graduating, I developed firmware and signal processing for an embedded ultrasound sensor. In January 2013 Petri offered me a place designing the lighting conditions and camera setup for the behavioral experiments. In addition to a little tinkering, I also have the option to investigate the different methods of tracking mice. Who could have refused?

Kata Holopainen

MSc Student

I am a Master's student in neuroscience who has always been drawn by the mysteries hiding inside the skull. The only way to understand the brain, in my opinion, is to take a look across all levels of organization, from individual cells to systems level processing, leading up to behavioral outcomes. Doing behavioral experiments with mice in Petri's lab has given me the opportunity to dive into research that is well conducted and has the ability to provide deeper understanding of brain processes through the visual system.

Alexandra Prinz

MSc Student

I am a passionate neuroscience and technology student at Aalto University, striving to understand the underlying mechanisms of our brain in the deepest possible level. In this lab, it is made possible by getting to work with great people, technologies and ideas.

Sami Minkkinen, MSc (Tech)

Laboratory Manager

I am a techie with a strong interest in science. I have a startup attitude and I like to design, create, and build both hardware and software. I have studied Engineering Physics, Biomedical Engineering, and Computer and Information Science at Aalto University. Besides this work, I have experience in programming, R&D, running a business, and patenting.

Janne Töykkälä, MSc

Research Assistant

I have a Master’s in neuroscience from Scotland/Germany and I am interested in how technology can interface with the brain. If it's neural and it can be directly recorded, I'm in. I am grateful to be fulfilling my non-military service in such a passionate lab as this.

Former Members

Tony Azevedo, PhD

Postdoctoral Fellow

Tony is a California native, born and raised in the Bay Area who did his B.S. at Berkeley (Engineering Physics, 2005) and PhD. at University of Washington (Physiology and Biophysics, 2011). Tony joined our lab for the summer and autumn of 2012 for a short but productive postdoc period before starting his current postdoctoral training at Harvard. Tony’s project continues as a collaboration.

Matthew Dunkerley

Programmer

I am a person that is trying to get the most out of life. After graduating University in Australia with an IT degree majoring in mathematics, I worked for 2 years as a Systems Engineer at the largest Google Enterprise partner in the Asia Pacific. This enabled me to travel across Australia and Indonesia and develop great business relations. After this I was conscripted to the Finnish military and have now lived in Finland for 2 years.

Sanna Koskela, PhD

PhD Candidate

I’ve always been fascinated by vision, in all its forms. After graduating in 2012 with a major in biology (University of Eastern Finland), I came to the University of Helsinki to learn more about neuroscience. Petri’s group provided the fascinating opportunity to study the visual system from single cells to behavior and to learn several valuable techniques.

Sathish Narayanan

Master's Student

I am pursuing my Master's in bioinformatics at Aalto University. My research interests center in understanding the computational principles of the brain. I have a strong appetite for programming. Before my Master’s I was working as a software developer, technical evangelist in Infosys, India (2006 - 2010).

Anna Stöckl, PhD

Postdoctoral Fellow

Throughout my scientific journey, I have been interested in how neural circuits process sensory information. During my PhD (2012-2016 at Lund University), I investigated visual neurons in the brain of hawkmoths to understand how they overcome the challenge of low signal and high noise levels their visual system faces at night. For my postdoc in Petri’s lab I will study how small populations of neurons in the mouse retina combat the noisy regimes their visual system faces in dim light, with particular focus on noise which is correlated between neurons of the population.

Daisuke Takeshita, PhD

Postdoctoral Fellow

I would like to understand how the brain works using a combination of experimental and computational techniques (note that the retina is an extension of the brain!).

Contact

Petri Ala-Laurila

Associate Professor
Department of Neuroscience and Biomedical Engineering
Aalto University School of Science
P.O. Box 12200 ( Rakentajanaukio 2C )
FI-00076 AALTO
Finland
Email: petri.ala-laurila@aalto.fi

Adjunct Professor (Neuroscience) & PI
Molecular and Integrative Biosciences Research Programme
Faculty of Biological and Environmental Sciences
P.O. Box 65 ( Viikinkaari 1 )
FIN-00014, University of Helsinki
Finland
Email: petri.ala-laurila@helsinki.fi

@AlaLaurilaLab @AlaLaurilaLab