Piotr Majka, Ph.D. Assistant Professor Laboratory of Neuroinformatics, Nencki Institute of Experimental Biology Pasteur 3 St., 02-093 Warsaw, Poland tel.: 48 22 5892 404 email: p.majka@nencki.edu.pl http://github.com/pmajka

Education

2014: Ph.D. in Neuroinformatics

Nencki Institute of Experimental Biology, Warsaw, Poland,
thesis: Integration of structural imaging data of gray short-tailed opossum brain,
graduated summa cum laude.

2004 - 2009: Master of Science in Engineering (applied physics)

Faculty of Physics, Warsaw University of Technology,
graduated with distinction.

Research interests

• Integration of multimodal and multiscale neuroanatomical image data. Application of statistical and machine learning methods to get insight from large–scale imaging datasets:
  • Mapping tracer injection studies and construction of a multimodal digital brain atlas of the marmoset monkey cerebral cortex.
• Biomedical image acquisition and processing, registration and reconstruction of 3D brain images based on serial sections:
  • Development of a open framework for three-dimensional reconstruction of brain images from serial sections - the Possum software (see the publication).
  • Creating multimodal stereotactic atlas of the Monodelphis domestica opossum brain (MRI and microCT, blockface images, Nissl and myelin histology). See: PhD thesis (in polish), YouTube videos: (1, 2), conference posters (1, 2, 3) and abstracts (1, 2, 3, 4).
• Digital (including three-dimensional) brain atlases construction and dissemination:
  
  • Membership in the International Neuroinformatics Coordinating Facility Program on Digital Brain Atlasing.
  • Developing a generic data format to store and distribute 2D atlas delineations and designing 3D Brain Atlas Reconstructor software.
  • Creating the 3dBAR web service, an online repository of three-dimensional models of brain structures (23 atlas datasets, 120 registered users as of March 2016). See: publication, video tutorials, API reference.

Prizes and Awards

Peer reviewed publications

• Teymornejad S., Majka P., Worthy K.H., Atapour N. Rosa M.G.P. (2024). Bilateral connections from the amygdala to extrastriate visual cortex in the marmoset monkey. Cerebral Cortex 34(9), bhae348, doi: 10.1093/cercor/bhae348.
• Reznik D., Majka P., Rosa M.G.P., Witter M.P., Doeller C.F. (2024). Phylogeny of neocortical-hippocampal projections provides insight in the nature of human memory.
  a eLife, 13:RP99203. doi: 10.7554/eLife.99203.1.
• Atapour N., Rosa M.G.P., Bai S., Bednarek S., Kulesza A., Saworska G., Teymornejad S., Worthy K., Majka P. (2024). Distribution of calbindin-positive neurons across areas and layers of the marmoset cerebral cortex. PLOS Computational Biology 20(9): e1012428. doi: 10.1371/journal.pcbi.1012428.
• Stefaniuk M., Pawłowska M., Barański M., Nowicka K., Zieliński Z., Bijoch Ł., Legutko D., Majka P., Bednarek S., Jermakow N., Wójcik D., Kaczmarek L. (2023). Global brain c-Fos profiling reveals major functional brain networks rearrangements after alcohol reexposure. Neurobiology of Disease, 178(January), 106006, doi: 10.1016/j.nbd.2023.106006.
• Tian X., Chen Y., Majka P., Szczupak D., Perl Y.S., Yen C.C.-C., Tong C., Feng F., Jiang H., Glen D., Deco G., Rosa M.G.P., Silva A.C., Liang Z., and Liu C. (2022). An integrated resource for functional and structural connectivity of the marmoset brain. Nature Communications, 13(1), 7416, doi: 10.1038/s41467-022-35197-2.
• Global Collaboration Workshop and Consortium: Milham M., Petkov C., (...) Klink C., Majka P., Mars R., (...) Zuo Z. (2021). Toward next-generation primate neuroscience: A collaboration-based strategic plan for integrative neuroimaging. Neuron, 110(1), 16–20, doi: 10.1016/j.neuron.2021.10.015.
• Bakola S., Burman K.J., Bednarek S., Chan J.M., Jermakow N., Worthy K., Majka P., Rosa M.G.P. (2021). Afferent Connections of Cytoarchitectural Area 6M and Surrounding Cortex in the Marmoset: Putative Homologues of the Supplementary and Pre-supplementary Motor Areas. Cerebral Cortex, bhab193, doi: 10.1093/cercor/bhab193.
• Theodoni P., Majka P., Reser D.H., Wójcik D.K., Rosa M.G.P. (2021). Structural Attributes and Principles of the Neocortical Connectome in the Marmoset Monkey, Cerebral Cortex, bhab191, doi: 10.1093/cercor/bhab191.
• Feizpour A., Majka P., Chaplin T.A., Rowley D., Yu H-H., Zavitz E., Price N.S.C., Rosa M.G.P. (2020). Visual responses in the dorsolateral frontal cortex of marmoset monkeys, Journal of Neurophysiology, doi: 10.1152/jn.00581.2020.
• Messinger A., Sirmpilatze N., Heuer K., Kee-Loh K., Mars R.B., Sein J., Xu T., Glen D., Jung B., Seidlitz J., Taylor P., Toro R., Garza-Villarreal G.A., Sponheim C., Wang X., Benn R.A., Cagna B., Dadarwal R., Evrard H.C., Garcia-Saldivar P., Giavasis S., Hartig R., Lepage C., Liu C., Majka P., Merchant H., Milham M.P., Rosa M.G.P., Tasserie J., Uhrig L. (2021). A collaborative resource platform for non-human primate neuroimaging, Neuroimage, 226, 117519, doi: 10.1016/j.neuroimage.2020.117519.
• Majka P., Bednarek S., Chan J.M., Jermakow N., Liu C., Saworska G., Silva A.C., Wójcik D.K., Rosa M.G.P. (2020). Histology-Based Average Template of the Marmoset Cortex With Probabilistic Localization of Cytoarchitectural Areas. Neuroimage 117625, doi: 10.1016/j.neuroimage.2020.117625.
• Majka P., Bai S., Bakola S., Bednarek S., Chan J., Jermakow N., Passarelli L., Reser D., Theodoni P., Worthy K., Wang X-J, Wójcik D., Mitra P.P., Rosa M.G.P. (2020). Open Access Resource for Cellular-Resolution Analyses of Corticocortical Connectivity in the Marmoset Monkey. Nat Comm, 11, 1133 (2020). doi: 10.1038/s41467-020-14858-0.
• Liu C., Ye F.Q., Newman J.D., Szczupak D., Tian X., Yen C.C., Majka P., Glen D., M.G.P Rosa., Leopold D.A., Silva A.C. (2020). A resource for the detailed 3D mapping of white matter pathways in the marmoset brain. Nat Neurosci 23, 271–280, doi: 10.1038/s41593-019-0575-0.
• The PRIMatE Data Exchange (PRIME-DE) Global Collaboration Workshop and Consortium (2020). Accelerating the Evolution of Nonhuman Primate Neuroimaging. Neuron 105(4) 600-603, doi: 10.1016/j.neuron.2019.12.023.
• Dolezyczek H., Tamborski S., Majka P., Sampson D.M., Wojtkowki M., Wilczynski G., Szkulmowski M., Malinowska M. (2020). In vivo brain imaging with multimodal optical coherence microscopy in a mouse model of thromboembolic photochemical stroke. Neurophotonics, 7(1), 015002, doi: 10.1117/1.NPh.7.1.015002.
• Goulas A., Majka P., Rosa M.G.P., Hilgetag C.C. (2019). A blueprint of mammalian cortical connectomes. PLOS Biology 17(3): e2005346., doi: 10.1371/journal.pbio.2005346.
• Atapour N., Majka P., Wolkowicz I.H., Malamanova D., Worthy K.H., Rosa M.G.P (2018). Neuronal Distribution Across the Cerebral Cortex of the Marmoset Monkey (Callithrix jacchus) Cerebral Cortex, bhy263, doi: 10.1093/cercor/bhy263.
• P. Majka, M.G.P. Rosa, S. Bai, J.M. Chan, B.-X. Huo, N. Jermakow, M.K. Lin, Y.S. Takahashi, I.H. Wolkowicz, K.H. Worthy, R. Rajan, D.H. Reser, D.K. Wójcik, H. Okano, P.P. Mitra (2018). Unidirectional monosynaptic connections from auditory areas to the primary visual cortex in the marmoset monkey. Brain Structure and Function (2018), doi: 10.1007/s00429-018-1764-4.
• Rosa, M.G.P., Soares J.G.M., Chaplin T.A., Majka P., Bakola S., Phillips K.A., Reser D.H., Gattass R. (2018). Cortical afferents of area 10 in Cebus monkeys: implications for the evolution of the frontal pole. Cerebral Cortex, doi: 10.1093/cercor/bhy044.
• Majka P., Chłodzińska N., Turlejski K., Banasik T., Djavadian R.L., Węglarz W. and Wójcik D.K. (2017). A three-dimensional stereotaxic atlas of the gray short-tailed opossum (Monodelphis domestica) brain. Brain Struct Funct (2017), doi: 10.1007/s00429-017-1540-x.
• Knauer B., Majka P., Watkins K.J., Taylor A.W.R., Malamanova D., Paul B., Reser D.H. (2017). Whole-brain metallomic analysis of the common marmoset (Callithrix jacchus). Metallomics, 9(4), 411–23, doi: 10.1002/cne.24023.
• Majka P., Chaplin T.A., Yu H., Tolpygo A., Mitra P., Wójcik D.K. and Rosa M. (2016). Towards a comprehensive atlas of cortical connections in a primate brain: Mapping tracer injection studies of the common marmoset into a reference digital template, Journal of Comparative Neurology, 11, 2161–81, doi: 10.1002/cne.24023.
• Reser D.H., Majka P., Snell S., Chan J., Watkins K., Worthy K., Quiroga M.D.M., Rosa, M.G.P. (2016). Topography of claustrum and insula projections to medial prefrontal and anterior cingulate cortex of the common marmoset (Callithrix jacchus). Journal of Comparative Neurology, doi: 10.1002/cne.24009.
• Majka, P., Wójcik, D. K. (2016). Possum - A Framework for Three-Dimensional Reconstruction of Brain Images from Serial Sections. Neuroinformatics, 14, 265–278. doi: 10.1007/s12021-015-9286-1.
• Setkowicz, Z., Gaździńska, A., Osoba, J. J., Karwowska, K., Majka, P., Orzeł, J., Kossowski, B., Bogorodzki, P., Janeczko, K., Wyleżoł, M., Gazdzinski, S.P. (2015). Does Long-Term High Fat Diet Always Lead to Smaller Hippocampi Volumes, Metabolite Concentrations, and Worse Learning and Memory? A Magnetic Resonance and Behavioral Study in Wistar Rats. Plos One, 10(10), e0139987, doi: 10.1371/journal.pone.0139987.
• Zakiewicz, I. M., Majka, P., Wójcik, D. K., Bjaalie, J. G., and Leergaard, T. B. (2015). Three-Dimensional Histology Volume Reconstruction of Axonal Tract Tracing Data: Exploring Topographical Organization in Subcortical Projections from Rat Barrel Cortex. PLOS ONE, 10(9), e0137571, doi: 10.1371/journal.pone.0137571.
• Majka, P., Kowalski, J. M., Chlodzinska, N., and Wójcik, D. K. (2013). 3D Brain Atlas Reconstructor Service-Online Repository of Three-Dimensional Models of Brain Structures. Neuroinformatics 11, 507–18, doi: 10.1007/s12021-013-9199-9.
• Majka, P., Kublik, E., Furga, G., and Wójcik, D. K. (2012). Common atlas format and 3D brain atlas reconstructor: infrastructure for constructing 3D brain atlases. Neuroinformatics 10, 181–97, doi: 10.1007/s12021-011-9138-6.

Employment history

Jul 2016 – ongoing: Assistant Professor,

Nencki Institute of Experimental Biology, Pasteur 3 St., 02-093 Warsaw, Poland.
Development of tools and models and using them to understand neural processing of sensory information in the brain. Application of statistical and machine learning methods to get insight from large–scale imaging datasets.

Jan 2015 – Jun 2016: Biomedical Software Engineer (Postdoctoral Research Fellow),

Jul 2016 – Jun 2021: Adjunct Research Associate,

Jul 2021 – ongoing: Adjunct Research Fellow.

Department of Physiology, Monash University, Melbourne, Australia.
Analysis and modeling of anatomical connections in the monkey brain. Designing and deploying a pipeline for terabyte-scale imaging data processing. End—user training.

Feb 2010 – Dec 2014: Scientific Software Developer / IT administrator

Laboratory of Neuroinformatics, Nencki Institute of Experimental Biology
Developing computational methods for analysis of 3D brain images. Deployment and administration of Linux-based desktops, servers, and computational cluster.

Aug 2011: System administrator

Advanded Course in Computational Neuroscience 2011 at Będlewo, Poland.
Setting up and running computer laboratory of 30 desktops during the shool (GNU/Linux, NFS, LDAP).

Jul 2007 – Jan 2010: Internet Analyst in the Gemius Audience Research Department

Gemius S.A., 7 Wołoska St., 02-675 Warsaw
Estimation of sociodemographic profiles and monitoring of traffic of websites and mobile applications. Delivering results to clients and implementing recommendations.

Proffesional skills

• Proficient in Python, Unix shell (BASH, awk, sed, etc.), HTML, JavaScript, Git, LaTeX; Competent in C/C++, PHP, SQL, Mathematica, ITK and VTK toolkits, various image processing and registration software, numerical and statistical packages for Python (SciPy, NumPy, Pandas, Seaborn, StatsModels)
• Deployment and administration of Linux-based desktops, servers and computational clusters, performing large scale computations.
• Managing small IT projects (up to 3 developers), designing scientific software and enforcing good practices in software development,

Trainings, internships and scientific visits (excluding conferences)

• 04.2018: Marco Tripodi Laboratory, MRC Laboratory of Molecular Biology; Cambridge, UK
• 10.2017: CAJAL course: Connectomics: from Micro- to Meso- and Macro-Scales; Bordeaux, France
• 09.2017: RIKEN Brain Science Institute; Riken, Japan
• 08.2015: Australian Research Council Centre of Excellence for Integrative Brain Function Early Career Researcher Workshop and Science and Node Administration Meetings, Cairns, Australia
• 05.2015: Australian Research Council Centre of Excellence for Integrative Brain Function and Human Brain Project Science Meeting, Monash University Campus, Prato, Italy.
• 05.2015: Neurophysiology and Neuroanatomy of the Visuo-Motor System, University of Bologna, Italy
• 11-12.2014: Penn Image Computing & Science Lab, University of Pennsylvania; Philadeplhia, USA.
• 10-11.2014: Department of Physiology, Monash University; Melbourne, Australia.
• 03.2014: Centre for Advanced Imaging - University of Queensland; Brisbane, Australia.
• 03.2014: Department of Physiology, Monash University; Melbourne, Australia.
• 7-8.2014: Mentor of the Real-time vectorization of brain atlases project during the Google Summer of Code 2014.
• 09.2013: participation in the INCF sponsored course Imaging the brain at different scales: how to integrate multi-­scale structural information?, Antwerp, Belgium.
• 08.2013: participation in the EIBIR Summer School on Neurology Imaging 2013, Dubrovnik, Croatia.
• 09.2012: participation in Advanced Python Summer School 2012; Kiel, Germany.
• 06.2012: participation in Allen Brain Atlas Hackathon 2012 organized by the Allen Institute for Brain Science; Seattle, USA.
• 05.2010: INCF travel grant for visiting Donders Institute for Brain, Cognition and Behavior; University Medical Centre St. Radboud; Nijmegen, The Netherlands. Creating a mechanism allowing for data exchange between Scalable Brain Atlas and 3d Brain Atlas Reconstructor by developing suitable converters and overcoming technical difficulties.
• 01.2010: participation in the Second Polish-Norwegian Neuroinformatics Workshop How to model neurons and neural systems? Integrating biophysics, morphology, and connectivity, Warsaw, Poland, January 14-15, 2010.

Participation in research projects

2026 – ongoing: Elucidating the principles of primate thalamocortical circuitry (2025/56/Q/NZ2/00227).

Principal Investigator.

2026 – ongoing: The Ageing Primate Brain: Molecular, Cellular and Systems-Level Insights (ARC DP260100324).

Partner Investigator.

2025 – 2026: Bringing Marmoset to EBRAINS.

Principal Investigator. EBRAINS 2.0 A Research Infrastructure to Advance Neuroscience and Brain Health (grant no. 101147319, Work Package 4) under the Financial Support to Third Parties (FSTP) funding scheme.

2020 – ongoing: Cortical circuitry following damage to the primate visual cortex (2019/35/D/NZ4/03031).

Principal Investigator.

2022 – ongoing: The effects of early exposure to bushfires on adult brain structure and function (APP2011733).

Principal Investigator: Dr Farshad Mansouri, function: Chief Investigator (CI, within the meaning of National Health and Medical Research Council Australia).

2017 – 2019: Enabling cellular-resolution connectomic analysis of the primate cortex.

Principal Investigator.

2017 – 2020: MICRONET: Cortical microcircuitry after traumatic brain injury: molecules to networks.

Investigator, PI: prof. Daniel Wójcik.

2016 – ongoing: Localization of epilepsy sources from clinical multimodal data using kernel methods.

Investigator, PI: prof. Daniel Wójcik, (2015/17/B/ST7/04123).

2015 – 2016: Understanding complex networks of connections in the primate cerebral cortex.

Investigator, PI: prof. Marcello Rosa, (DP140101968).

2015 – 2021: Australian Research Council Centre of Excellence for Integrative Brain Function.

Primary Chief Investigator: prof. Gary Egan, function: investigator, (CE140100007).

2010 – 2014: "Biocentrum Ochota" project funded by European Regional Development Fund under the Operational Programme Innovative Economy.

Investigator, Task PI: prof. Daniel Wójcik, (POIG.02.03.00-00-003/09).

2009 – 2010: Środowisko obliczeniowe do wykrywania i analizy relacji przyczynowości w symulacjach układów biomolekularnych i nanoukładów metodami dynamiki molekularnej.

Investigator, PI: prof. Bogdan Lesyng, (3847/B/T02/2009/36, reg. no.: NN519384736).

Talks and lectures

• Majka P. (2025). Bringing Marmoset to EBRAINS. During the User Talks session: cutting-edge work that leverages the power of EBRAINS. EBRAINS Summit 2025, Brussels 8-11 December 2025 (invited speaker).
• Majka P. (2025). Digital neuroanatomy, why and how? Cortico-cortical connectivity atlas of the common marmoset (Callithrix jacchus). Flash talk at PRIMatE Resource Exchange (PRIME-RE) Global Collaboration Forum, 4–5 December 2025, online meeting.
• Majka P., G. Santpere, K. Dong Won, Xie P., Sub Y., Zhu Y. (2025). Interactome, panel discussion. International Forum on Mesoscopic Brain Mapping, Shanghai, 20–21 September 2025 (invited speaker).
• Majka P. (2025). Digital neuroanatomy, why and how? 17^th International Congress of the Polish Neuroscience Society, Wrocław, 2–5 September 2025 (invited speaker during plenary session).
• Majka P. (2025). Artificial intelligence in digital neuroanatomy. 6^th Central European Biomedical Congress, Kraków 22-24 July 2025 (invited speaker).
• Majka P. (2025). Bringing Marmoset to EBRAINS. EBRAINS Co-Design meeting, 10 June 2025 (online meeting).
• Majka P. (2025). Cortico-cortical connectivity atlas of the common marmoset (Callithrix jacchus). Nencki Institute Scientific Council Report Session, Warsaw, 28 February 2025 (invited speaker).
• Majka P. (2023). Deep learning approaches in observer-independent exploration of cytoarchitectural properties of the non-human primate cerebral cortex. 16^th International Congress of the Polish Neuroscience Society, Toruń, 20–23 September 2023.
• Majka P. (2022): The Marmoset Brain Connectivity Atlas: An open access resource for analysis of connections in the primate cortex (invited speaker during plenary session).
  2^nd International Workshop on Marmoset Neuroscience, 8 July 2022, Institut de Neurosciences de la Timone, Marseille, France.
• Majka P. (2021): The Marmoset Brain Connectivity Atlas: An open access resource for analysis of connections in the primate cortex. Symposium of the TEAM NET FNP project "Bio-inspired artificial neural networks", 5 October 2021. Faculty of Mathematics and Computer Science of the Jagiellonian University, Cracow, Poland (invited speaker).
• Majka P. (2021): Połączenia korowe ssaków naczelnych po uszkodzeniach pierwszorzędowej kory wzrokowej - Doktorat w Pracowni Neuroinformatyki IBD PAN. Presentation for Science Clubs:
  • 15.04.2021: Studenckie Koło Naukowe Fizyków Fusion.
  • 19.04.2021: Koło Naukowe Biofizyki Molekularnej i Fizyki Medycznej.
  • 21.04.2021: Studenckie Koło Naukowe Neuronus.
  • 26.04.2021: Koło Matematyków Studentów UJ.
• Majka P. (2019): Open Access Resource for Cellular-Resolution Corticocortical Connectivity in the Marmoset Monkey. International Neuroinformatics Coordinating Facility "Neuroinformatics 2019" conference, 1 September 2019, Faculty of Physics, University of Warsaw, Poland (invited speaker during plenary session).
• Majka P. (2019): The Marmoset Brain Connectivity Atlas: An open access resource for analysis of connections in the primate cortex. "Brains United" workshop, 30 August 2019, Faculty of Physics, University of Warsaw, Poland (invited speaker).
• Majka P. (2019): The Marmoset Brain Connectivity Atlas: An open access resource for analysis of connections in the primate cortex. 14^th International Congress of the Polish Neuroscience Society, 28–30 August 2019, Katowice, Poland.
• Majka P. (2019): Symposium "Workshop on imaging of optically cleared preparations (lightsheet)". Nencki Institute of Experimental Biology PAS, 21 May 2019, Nencki Institute of Experimental Biology PAS, Warsaw, Poland (invited speaker).
• Majka P. (2019): Location, location, location. The role of brain atlases and spatial integration of multimodal imaging data in whole brain mapping projects. Center for Translational Imaging (MoMAN) Seminar, 9 January 2019, Ulm University, Ulm, Germany (invited speaker).
• Majka P. (2018): Towards a cellular-resolution connectome of the primate brain: sharing the data on corticocortical connectivity through an open access web platform. Workshop “2^nd Polish-Czech workshop on translational neuroinformatics and brain imaging in psychedelic research”, 8 September 2018, National Institute of Mental Health, Prague, Czech Republic.
• Majka P. (2018): How can the INCF Seed Funding help your project thrive?. Meeting of the Polish Node of the International Neuroinformatics Coordinating Facility, 18 September 2018. Jagiellonian University, Cracow, Poland.
• Majka P. (2018): The network organisation of the marmoset cerebral cortex: large-scale analysis of cortico-cortical connections at single cell resolution. 4^th International Conference The Marmoset in Neuroscience, 22 March 2018; Institut de Neurosciences de la Timone, Marseille, France (invited speaker during plenary session).
• Majka P. (2017): A Marmoset Connectome for Area-Based and Parcellation-Free Connectivity Analysis. RIKEN Brain Science Institute, Riken; Japan (invited speaker).
• Majka P. (2017): Mesoscopic, inter-areal connectome of marmoset monkey cortex. Comparison with mouse and macaque monkey connectomes. Plasticity of the nervous system after external insults: From molecules to networks. MICRONET Consortium Meeting. 12 Jun 2017, Nencki Institute of Experimental Biology, Warsaw, Poland.
• Majka P. (2017): Brain Cartography: How novel imaging methods and high-throughput computational techniques help in modern neuroanatomy and neurophysiology. The first Polish-Czech workshop on translational neuroinformatics and brain imaging in psychedelic research. 3 March 2017, Nencki Institute of Experimental Biology, Warsaw, Poland.
• Majka P. (2017): Kartografia mózgu. Jak nowoczesne metody obrazowania i techniki obliczeniowe pomagają w zrozumieniu struktury i funkcji mózgu. Seminarium Zakładu Fizyki Biomedycznej UW. 12 January 2017, Warsaw, Poland.
• Majka P. (2016): Large scale marmoset monkey cerebral cortex connectivity mapping. Seminar of the Department of Neurophysiology, 22 June 2016; Nencki Institute of Experimental Biology, Warsaw; Poland.
• Majka P. (2015): Developing a cellular-resolution connectome of the marmoset brain: Platform for integration, visualisation, sharing and analysis of marmoset connectivity data. Australian Research Council Centre of Excellence for Integrative Brain Function Early Career Researcher Workshop and Science and Node Administration Meetings. 18-19 August 2015, Cairns, Queensland, Australia.
• Majka P. (2015): Workflows for histology – based reconstructions of 3D brain images. Australian Research Council Centre of Excellence for Integrative Brain Function and Human Brain Project Science Meeting, 27-29 May 2015, Monash University Campus, Prato, Italy.
• Majka P. (2014): Integration of multimodal structural imaging data of gray short-tailed opossum brain. Centre for Advanced Imaging University of Queensland, Brisbane; Australia.
• Majka P. (2014): Multimodal stereotactic template of the gray short-tailed opossum brain. Department of Physiology, Monash University, Melbourne; Australia
• Majka P. (2012): The Scalable Brain Atlas and the 3d Brain Atlas Reconstructor, presentation during the Joint MRC/INCF/SICSA Workshop on Atlas Informatics; Edinburgh, 15–16 May 2012,
• Majka P. (2011): 3D Brain Atlas Reconstructor and Common Atlas Format, the infrastructure for constructing three dimensional brain atlases, presentation during the Python in Neuroscience 2011 Conference. Ecole Normale Supérieure, 29–30 August 2011, Paris, France.
• Majka P. (2009): Causality Analysis of Molecular Dynamics Events with Mathematica 7, presentation during the Poland Mathematica Conference 2009. 25–26 May 2009, Kraków, Poland.

Abstracts and conference proceedings

• Majka P., Bai S., Datta A., Łabuszewska K., Syc M., Walkiewicz T., Rosa M.G.P. (2025). Bringing Marmoset to EBRAINS. 17^th International Congress of the Polish Neuroscience Society, Wrocław, September 2-5^th 2025, poster no. P2.45 (see the poster).
• Datta A., Kulesza A., Syc M., Rosa M.G.P, Majka P. (2025). Characterization of the cerebral cortex in the non-human primate brain: a deep learning model interpretability approach.
  17^th International Congress of the Polish Neuroscience Society, Wrocław, September 2-5^th 2025, poster no. P1.48 (see the poster).
• Datta A., Kulesza A., Syc M., Rosa M.G.P, Majka P. (2025). Characterization of the cerebral cortex in the non-human primate brain: a deep learning model interpretability approach.
  9^th International PhD Students Conference at Nencki Institute of Experimental Biology, Warsaw, October 7-9^th 2025 (see the poster).
• Datta A., Kulesza A., Bednarek S., Rosa M.G.P., Majka P. (2024). Towards objective characterization of the cerebral cortex cytoarchitecture: a deep-learning workflow for identifying and segmenting cortical areas. Neuronus 2024 Neuroscience Forum, Crackow, April 25-27^th 2024 (abstract book, see the poster).
• Majka P., Atapour N., Rosa M.G.P., Bai S., Bednarek S., Kulesza A., Saworska G., Teymornejad S., Worthy K.H. (2024). Distribution of Calbindin positive neurons across areas and layers of the marmoset cerebral cortex. Neuronus 2024 Neuroscience Forum, Crackow, April 25-27^th 2024 (abstract book, see the poster).
• Jakubowska J., Bednarek S., Saworska G., Rosa M.G.P., Majka P. (2024). Observer-independent workflow for cytoarchitectural characterization of neural tissue using variational autoencoder architecture. Neuronus 2024 Neuroscience Forum, Crackow, April 25-27^th 2024 (abstract book, see the poster).
• Majka P., Datta A., Kulesza A., Bednarek S., Rosa M.G.P. (2024). An explainable deep learning model for the indentification of layers and areas in the primate cerebral cortex. FENS Forum 2024, Vienna, June 25-29^th 2024, poster no. PS01-26AM-518 (see the poster).
• Datta A., Kulesza A., Bednarek S., Rosa M.G.P., Majka P. (2024). Towards objective characterization and interpretation of cytoarchitectural properties of the primate cerebral cortex. Aspects of Neuroscience 2024, Warsaw, October 27^th 2024, (abstract book, see the poster).
• Kulesza A., Bednarek S., Rosa M.G.P., Majka P. (2023). Deep learning approaches to identification of cortical areas in the marmoset cortex. 16^th International Congress of the Polish Neuroscience Society, Toruń, 20-23 September 2023, poster no. P15.1 and flashtalks' session (abstract book, see the poster).
• Datta A., Kulesza A., Bednarek S., Rosa M.G.P., Majka P. (2023). Deep learning approaches in observer-independent exploration of cytoarchitectural properties of the non-human primate cerebral cortex. 16^th International Congress of the Polish Neuroscience Society, Toruń, 20-23 September 2023, poster no.: P15.3 (abstract book, see the poster).
• Datta A., Kulesza A., Bednarek S., Rosa M.G.P., Majka P. (2023). Towards the observer-independent analyses of cytoarchitectural properties of the mammalian cerebral cortex. Aspects of Neuroscience 2023, Warsaw, March 24-26.
• Kulesza A., Bednarek S., Saworska G., Rosa M.G.P., Majka P. (2022). Deep learning approaches to identification and delineation of cortical areas in the marmoset cortex. Society for Neuroscience 2022, Nov 11-17, San Diego, program no. 328.03 / YY25 (show the abstract, see the poster).
• Skibbe H., Rachmadi M.F., Nakae K., Gutierrez C.E., Hata J., Tsukada H., Poon C., Doya K., Majka P., Rosa M.G.P., Okano H., Yamamori T., Ishii Sh., Reisert M., Watakabe A. (2022). The Brain/MINDS Marmoset Connectivity Atlas. Society for Neuroscience 2022, November 11-17, San Diego, program no. 328.02 / Web Only (show the abstract).
• Atapour N., Bednarek S., Kulesza A., Saworska G., Worthy K.H., Majka P., Rosa M.G.P. (2022). Distribution of calbindin-immunoreactive neurons throughout the entire cerebral cortex of the marmoset (Callithrix jacchus). Society for Neuroscience 2022, Nov 11-17, San Diego, program no. 328.01 / YY24 (show the abstract, see the poster).
• Stefaniuk M., Pawłowska M., Barański M., Majka P., Kaczmarek L. (2022). Global Brain c-Fos Profiling and Functional Brain Networks Rearrangements After Alcohol Reexposure in Animal Model of Addiction. 46^th Annual Research Society on Alcoholism Scientific Meeting (Program ID: 122).
• Bednarek S., Jermakow N., Stefaniuk M., Pawłowska M., Rehman R., Nowicka K., Bijoch L., Roselli F., Wójcik D.K., Majka P. (2019). LSFMPy: open-source toolkit for brain-wide neural activity mapping in optically cleared mouse brain. Society for Neuroscience 2019, Oct 19-23, Chicago, program no. 505.11 (show the abstract, see the poster).
• Majka P., Atapour N., Bednarek S., Kulesza A., Saworska G., Worthy K.H., Rosa M.G.P. (2022). Mapping the distribution of neurochemically-defined cell types throughout the primate cortex. International Neuroinformatics Coordinating Facility Neuroinformatics Assembly 2022. September 12-16 2022 Virtual Conference (show the abstract).
• Bednarek S., Stefaniuk M., Pawłowska M., Nowicka K,. Kaczmarek L., Wójcik D.K., Majka P. (2021). Facilitating spatial integration of whole brain imaging data with deep learning. International Neuroinformatics Coordinating Facility Neuroinformatics Assembly 2021. April 19-29.2021 Virtual Conference (show the abstract).
• Majka P., Bednarek S., Chan M.C., Jermakow N., Liu C., Saworska G., Worthy K.H., Silva A.C., Wójcik D.K., Rosa M.G.P. (2021). Histology-based Average Template of the Marmoset Cortex with Probabilistic Localization of Cytoarchitectural Areas. International Neuroinformatics Coordinating Facility Neuroinformatics Assembly 2021. April 19-29.2021 Virtual Conference (show the abstract, see the poster).
• Nowicka K., Stefaniuk M., Pawłowska M., Legutko D., Protokowicz K., Bednarek S., Majka P., Kaczmarek L. (2020). Physiological and pathological appetitive learning – can we understand addiction by peeking inside the brain? Neuronus 2020 IBRO Neuroscience Forum, Dec. 8-11.
• Nowicka K., Stefaniuk M., Legutko D., Pawłowska M., Protokowicz K., Bednarek S., Jermakow N., Majka P., Kaczmarek L. (2020). Appetitive learning: from the whole brain to a single cell perspective 22^nd EMBL PhD Symposium: The Roaring 20s: A New Decade for Life Sciences Nov. 27-28.
• Nowicka K., Stefaniuk M., Legutko D., Zieliński Z., Pawłowska M., Bednarek S., Jermakow N., Majka P., Kaczmarek L. (2020). Appetitive learning: from the whole brain to a single cell perspective FENS Virtual Forum 2020, June 11-15.
• Bednarek S., Jermakow N., Stefaniuk M., Pawłowska M., Rehman R., Roselli F., Wójcik D.K., Majka P. (2019). Computational framework for whole volume analysis of optically cleared brains. Neuroinformatics 2019, Sep 1-2, Warsaw, Poland (show the abstract book, see the poster).
• Goulas A., Majka P., Rosa M.G.P., Hilgetag C.C. (2019). A blueprint of mammalian cortical connectomes. Neuroinformatics 2019, Sep 1-2, Warsaw, Poland (show the abstract book).
• Bednarek S., Jermakow N., Stefaniuk M., Pawłowska M., Wójcik D.K., Majka P. (2019). Whole-brain mapping of neuroplasticity in different experimental paradigms in mice - a computational perspective. 14^th International Congress of the Polish Neuroscience Society, Aug 28-30, Katowice, Poland
• Stefaniuk M., Nowicka K., Bijoch L., Zielinski Z., Bednarek S., Majka P., Kaczmarek L. (2019). Alcohol addicted brain mapping and imaging using light­sheet fluorescence microscopy. 44^th FEBS Congress, Jul 6-11, Kraków, Poland
• Grymanowska A.W., Martin A., Olszyński K.H., Nowiński K., Borucki B., Majka P., Bednarek S., Wilczyński G.M., Magalska A., Filipkowski R.K. (2019). Distinct nuclear architecture of neural stem cells among other neural cell types in adult hippocampal neurogenesis. 2019 Eurogenesis Meeting, Jun 11-13, Bordeaux, France
• Majka P., Bednarek S., Jermakow N., Legutko D., Pawłowska M., Stefaniuk M., Wójcik D.K. (2019). Computational infrastructure for managing and processing high-resolution 3D imaging datasets. Mid-term symposium of the ERA-NET NEURON, Jan 21-23; Bonn, Germany (see the poster).
• Atapour N., Majka P., Wolkowicz I.H., Malanova D., Worthy K. Rosa M.G. (2018). Neuronal density across the cerebral cortex of the marmoset monkey (callithrix jacchus). Society for Neuroscience 2018, Nov 3-7, San Diego, program no. 364.08. (show the abstract).
• Liu C., Ye F., Yen C., Newman J.D., Glen D., Majka P., Szczupak D., Guy J., Ha S., Leopold D.A., Rosa M.G. Silva A.C. (2018). NIH marmoset brain atlas v2.0: Using ultra-high-resolution diffusion MRI and a cortical tracing database to map white matter pathways. Society for Neuroscience 2018, Nov 3-7, San Diego, program no. 364.03. (show the abstract).
• Majka P., Theodini P., Reser D.H., Rosa M.G., Wang X.-J. (2017). Mesoscopic inter-areal connectivity of marmoset cortex: Comparison with mouse and macaque monkey. Society for Neuroscience 2017, Nov 11-15, Washington, program no. 346.02 / WW22 (show the abstract, see the poster).
• Rosa M.G., Majka P., Takahashi Y., Worthy K.H., Lin M.K., Wolkowicz I.H., Tolpygo A.S., Bai S., Huo B., Chan J.M., Sasaki E., Reser D.H., Okano H., Mitra P.P., (2017). Monosynaptic connections between auditory and visual areas in the marmoset monkey. Society for Neuroscience 2017, Nov 11-15, Washington, program no. 775.16 / EE5 (show the abstract).
• Bednarek S., Majka P. (2017). A data model for managing and processing high resolution three-dimensional datasets from whole-brain imaging. 6^th International Conference Aspects of Neuroscience, Warsaw, 24-26^th November.
• Śmigielski M., Majka P. (2017). Mathematical model of cortico-cortical interareal connection trajectories as geodesics in brain image. 6^th International Conference Aspects of Neuroscience, Warsaw, 24-26^th November.
• Majka P., Chan J.M., Bai S., Hutler-Wolkowicz Ianina., Jermakow N., Rosa M.G.P. (2017). Marmoset Connectome for Area-Based and Parcellation-Free Connectivity Analysis. 16^th International Neuroinformatics Coordinating Facility Nodes Workshop, Oslo, May 29-30.
• Majka P., Chan J.M., Bai S., Hutler-Wolkowicz Ianina., Jermakow N., Rosa M.G.P. (2017). Enabling cellular-resolution connectomic analysis of the primate cortex: sharing data on cortico-cortical connectivity through an open access web platform. 2^nd Nencki Symposium on Neurons in action. Warsaw, May 25-26 (poster).
• Knauer B., Hare D.J., Paul B., Yu H., Watkins K.J., Malamanova D., Majka P., Rosa M.G.P. Reser D.H. (2016). Cerebral distribution of trace elements in the common marmoset. Australasian Neuroscience Society Annual Scientific Meeting 2016, Dec 4-7 Hobart, poster 200 (show the abstract).
• Chan J.M., Majka P., Mitra, P.P., Ferrante D., Bai S., Rosa M.G.P. (2016). Towards a cellular-resolution connectome of the primate brain: sharing the data on corticocortical connectivity through an open access web platform. Australasian Neuroscience Society Annual Scientific Meeting 2016, Dec 4-7 Hobart, poster 67 (show the abstract).
• Reser D.H., Knauer B., Majka P., Chan J.M., Watkins K.J., Worthy K., Quiroga M.D.M., Rosa M.G.P. (2016). Claustrum connections of posterior cingulate regions in the marmoset cerebral cortex. Society for Neuroscience 2016, Nov 12-16, San Diego, program no. 779.09 / D33 (show the abstract).
• Knauer B., Hare D.J., Paul B., Majka P., Rosa M.G.P., Reser D.H. (2016). Toward a comprehensive metallome of the marmoset brain: manganese, iron, copper, and zinc distribution in the cerebral cortex. Society for Neuroscience 2016, Nov 12-16, San Diego, program no. 515.16 / BB10 (show the abstract).
• Rosa M.G.P., Majka P., Chan J.M., Bai S., Ferrante D., Mitra, P.P. (2016). The marmoset brain architecture project: sharing data on primate corticocortical connectivity through an open access web platform. Society for Neuroscience 2016, Nov 12-16, San Diego, program no. 291.05 (show the abstract).
• Majka P. and Wójcik D.K. (2016). Three-dimensional reconstruction of brain images from serial sections using the Possum framework. Front. Neuroinform. Conference Abstract: Neuroinformatics 2016. (doi:https://wos-api.clarivate.com/api/wos10.3389/conf.fninf.2016.20.00053). Show the poster.
• Majka P., Chaplin T.A., Yu H., Tolpygo A., Mitra P., Wójcik D.K. and Rosa M. (2015). Workflow for mapping tracer injection studies of the common marmoset into a reference template. Society for Neuroscience 2015, Oct 17-21, Chicago, program no. 450.02 (show abstract, see the poster).
• Reser D.H., Majka P., Chan J.M.H., Pham X., Watkins K.J., Snell S., Richardson K. and Rosa M.G.P. (2015). Claustrum connections with hubs of the default mode, salience, and frontoparietal networks in the common marmoset. Society for Neuroscience 2015, Oct 17-21, Chicago, program no. 563.06 (show).
• Gazdzinski, S.P., Setkowicz, Z., Osoba, J., Karwowska, K., Majka, P., Orzeł, J., Kossowski, B., Bogorodzki, P. (2015). A case of beneficial effects of high fat diet on the brain: a magnetic resonance and behavioral study in Wistar rats. Magnetic Resonance Materials in Physics, Biology and Medicine 2015, 32^nd Annual Scientific Meeting, Edinburgh, UK, 1-3 October. Abstract No.: S315, (doi: 10.1007/s10334-015-0489-0).
• Majka, P., Setkowicz, Z., Gazdzinski, S.P. (2015). Voxel-wise analyses of high-fat diet on brain structure in Wistar rats Magnetic Resonance Materials in Physics, Biology and Medicine 2015, 32^nd Annual Scientific Meeting, Edinburgh, UK, 1-3 October Abstract No.: S397, (doi: 10.1007/s10334-015-0489-0).
• Majka P., Chaplin T.A., Yu H., Pinskiy V., Mitra P., Wójcik D.K. and Rosa M. (2015). Workflow for mapping tracer injection studies of the common marmoset into a reference template. Front. Neurosci. Conference Abstract: Neuroinformatics 2015. doi: 10.3389/conf.fnins.2015.91.00022.
• Rosa M., Majka P., Chaplin, T., Yu H.-H., Wójcik D, Mitra P. (2015). Mapping neural connections in primates – an expanding role for cortical connectivity atlases. 25^th Biennial Meeting of the International Society for Neurochemistry jointly with the 13^th Meeting of the Asian-Pacific Society for Neurochemistry in conjunction with the 35^th Meeting of the Australasian Neuroscience Society. August 23–27 2015, Cairns, Australia. Abstract No.: S28-03, doi: 10.1111/jnc.13189.
• Reser D., Chan J., Watkins K., Majka P., Snell S., Pham X., Worthy K., Malamanova D., Rosa M. (2015). Claustrum projections to cingulate and medial prefrontal cortex of the marmoset (Callithrix jacchus). 25th Biennial Meeting of the International Society for Neurochemistry jointly with the 13th Meeting of the Asian-Pacific Society for Neurochemistry in conjunction with the 35th Meeting of the Australasian Neuroscience Society. August 23–27 2015, Cairns, Australia. Abstract No.: WTH19-08, doi: 10.1111/jnc.13189.
• Boline J.K., Baldock R., Bakker R., Burger A., Gee J., Haselgrove C., Hawrylycz M., Hess A., Johnson G.A, Majka P., Ng L., Okamura-Oho Y., Ruffins S. Zaslavsky I. (2014). Building access to the INCF digital atlasing infrastructure. Society for Neuroscience 2014, Nov 15-19, Washington, DC, program no. 371.09 (show).
• Majka P., Chłodzińska N., Banasik T., Djavadian R.L., Węglarz W., Turlejski K. and Wójcik D.K. (2014). Multimodal stereotactic atlas of gray short-tailed opossum's brain. Society for Neuroscience 2014, Nov 15-19, Washington, DC, program no. 185.22 (show).
• Majka P., Chaplin T.A., Yu H., Pinskiy V., Mitra P., Rosa M. and Wójcik D.K. (2014). Automated workflow for mapping tracer injection studies of the common marmoset into a reference template. Front. Neuroinform. Conference Abstract: Neuroinformatics 2014. doi: 10.3389/conf.fninf.2014.18.00038.
• Gazdzinski S.P., Setkowicz Z., Osoba J., Karwowska K., Majka P., Orzeł J., Kossowski B., Bogorodzki P., Kamińska M., Fiedorowicz M., Grieb P. (2014). Is high-fat high-carbohydrate diet (HFCD) neuroprotective? A magnetic resonance imaging study in Wistar rats. European Journal of Neurology Meeting Abstract PP1007, Volume: 21 Special Issue: SI Pages: 391-391 Supplement: 1, doi: 10.1111/ene.12497.
• Boline J., Baldock R., Bakker R., Burger A., Gee J., Haselgrove C., Hawrylycz M., Hess A., Johnson G., Majka P., Ng L.L., Okamura-Oho Y., Rufffins S.W. and Zaslavsky I. (2014). Growing the INCF Digital Atlasing Infrastructure. Front. Neuroinform. Conference Abstract: Neuroinformatics 2014. doi: 10.3389/conf.fninf.2014.18.00039.
• Majka P., Chlodzinska N., Banasik T., Djavadian R., Węglarz W., Turlejski K. and Wójcik D.W. (2013). Deformable coregistration of multimodal imaging data of gray short-tailed opossum brain. Front. Neuroinform. Conference Abstract: Imaging the brain at different scales: How to integrate multi-scale structural information?, Antwerp, Belgium, Sep 2-6, doi: 10.3389/conf.fninf.2013.10.00026.
• Majka P., Chlodzinska N., Banasik T., Djavadian R., Węglarz W., Turlejski K. and Wójcik D.K., (2013). Multimodal stereotactic template of the gray short-tailed opossum's brain. Neuroinformatics 2013 Congress. Stockholm, Sweden, August 27-29, doi: 10.3389/conf.fninf.2013.09.00021.
• Chaplin T.A., Yu H., Majka P., Yen C.C., Bakola S., Kowalski J.M., Hung C., Burman K.J., Wójcik D.K., Silva A.C. and Rosa M.G. (2013). Mapping the marmoset monkey cortex and the construction of a multimodal digital atlas. Neuroinformatics 2013 Congress. Stockholm, Sweden, August 27-29, doi: 10.3389/conf.fninf.2013.09.00122.
• Boline J., Avants B., Baldock R., Bakker R., Burger A., Gee J., Haselgrove C., Hess A., Ibanez L., Larson S., Majka P., Okamura-Oho Y, Ruffins S., Zaslavsky I. (2012). Registration workflows for the creation of INCF digital atlas hubs; Society for Neroscience Meeting. New Orleans; October 13-17.
• Majka P., Chlodzinska N., Banasik T., Djavadian R.L., P. Węglarz W., Turlejski K., Wójcik D.K., (2012). Integration of multimodal neuroanatomical data of gray short-tailed opossum; INCF Neuroinformatics 2012 Congress. Munich; September 10-12 (http://goo.gl/Epsoe).
• Boline J., Avants B., Baldock R., Bakker R., Burger A., Gee J., Haselgrove C., Hess A., Ibanez L., Larson S., Majka P., Okamura-Oho Y, Ruffins S., Zaslavsky I., (2012). Registration workflows for the creation of INCF digital atlas hubs. INCF Neuroinformatics 2012 Congress; Munich; September 10-12.
• Chlodzinska N., Majka P., Banasik T., Djavadian R.L., Weglarz W.P., Wojcik D.K., Turlejski K., (2012), System of anatomical data collection for the atlas of the opossum Monodelphis domestica brain. 8^th FENS Forum of Neuroscience; Barcelona; 14-18 July.
• Majka P., et al. (2012): Serving three-dimensional models of brain structures online, Front. Neuroinform. Conference Abstract: 4th INCF Congress of Neuroinformatics, Boston, 4-6 September.
• Majka P., et al. (2011): 3D Brain Atlas Reconstructor and Common Atlas Format, the infrastructure for constructing three dimensional brain atlases, Python in Neuroscience satellite to Euroscipy; Paris, Ecole Normale Supérieure, 29-30 August.
• Majka P., et al. (2010): Automated reconstruction of three-dimensional brain structures based on 2D histological atlases. Front. Neurosci. Conference Abstract: Neuroinformatics 2010. doi: 10.3389/conf.fnins.2010.13.00028.
• Bakker R., Larson S.D., Strobelt S., Hess A., Wójcik D., Majka P. and Kötter R. (2010): Scalable Brain Atlas: From Stereotaxic Coordinate to Delineated Brain Region Front. Neurosci. Conference Abstract: Neuroinformatics 2010. doi: 10.3389/conf.fnins.2010.13.00028.

Languages

• Polish - native,
• Fluent in spoken and written English (IELTS 8.0),
• Basic German and Russian.

Hobbies

References

Prof. Daniel K. Wójcik (d.wojcik@nencki.gov.pl)

Laboratory of Neuroinformatics, Head
Nencki Institute of Experimental Biology
3 Pasteur St, 02-093 Warsaw, Poland

Professor Marcello Rosa (marcello.rosa@monash.edu)

Monash Biomedicine Discovery Institute
Department of Physiology
Neuroscience Program
26 Innovation Walk,
Monash University, Clayton campus
Victoria 3800 Australia

Dr Rembrandt Bakker (r.bakker@donders.ru.nl)

Donders Institute for Brain, Cognition and Behavior
Montessorilaan 3
6525 HR Nijmegen
The Netherlands