Career Profile

PhD student at Uppsala University, specializing in the dynamic field of computerized image processing. My research primarily revolves around image and data analysis, with a specific emphasis on spatial transcriptomics and tissue architecture.

Experiences

Researcher

Sep 2015 - Aug 2017
Brno University of Technology, Czech republic

Research topics:

  • Signal processing of ECG
  • Localization of Epileptic Microseizures by Regression-Convolutional Neural Network System

Erasmus Exchange Student in Applied Physics

Sep 2017 - Jun 2018
University of Eastern Finland

Researcher

Oct 2017 - May 2018
University of Eastern Finland

Research topic: ECG noise level estimation

Researcher

Jan 2019 - Aug 2020
A.I. Virtanen Institute, Finland

Research topics:

  • Automated 3D Segmentation and Morphometry of Myelinated Axons in Grey Matter
  • Automated algorithm for segmentation of the cell’s cytosol and nuclei in images acquired with fluorescence microscopy
  • Implementation of UNet for segmentation for adenoviruses and debris in miniTEM images

Internship

Jan 2020 - May 2020
Uppsala University, Sweden

Research topic: Developing computational strategies to improve the quality and resolution of electron microscopy image acquisition

Researcher

Sep 2020 - Present
Uppsala University, Sweden

Research topic: Research project on topic Image and data analysis for spatial transcriptomics and tissue architecture.

Internship

September 2023
EMBL Rome, Italy

Research topic: Implementing an image analysis pipeline to profile the patterns of expression of 200 murine olfactory receptor genes in a single nasal epithelium of a mouse.

Teaching experience

Medical informatics

Uppsala University, Sweden

Computer-Assisted Image Analysis I

Uppsala University, Sweden

Deep Learning for Image Analysis

Uppsala University, Sweden

Deep Learning (DL) PhD course

Uppsala University, Sweden

Other Activities

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PhD representative - 2022-Present
Trainer in Scifest 2021 - Spring 2021

Publications

List of publications:

  • Cell Segmentation of in situ Transcriptomics Data Using Signed Graph Partitioning
  • A. Andersson*, A. Behanova*, C. Wählby, F. Malmberg
    Lecture Notes in Computer Science, Springer, 2023
  • TissUUmaps 3: Interactive visualization and quality assessment of large-scale spatial omics data
  • N. Pielawski, A. Andersson, C. Avenel, A. Behanova, E. Chelebian, A. Klemm, F. Nysjö, L. Solorzano, C. Wählby
    Heliyon, CellPress, 2023
  • Visualization and quality control tools for large-scale multiplex tissue analysis in TissUUmaps3
  • A. Behanova, C. Avenel, A. Andersson, E. Chelebian, A. Klemm, L. Wik, A. Ostman, C. Wahlby
    Biological Imaging, Cambridge University Press, 2023
  • Points2regions: Fast Interactive Clustering Of In Situ Transcriptomics Data
  • A. Andersson*, A. Behanova*, C. Avenel, C. Wählby, F. Malmberg
    bioRxiv, 2022
  • gACSON software for automated segmentation and morphology analyses of myelinated axons in 3D electron microscopy
  • A. Behanova, A. Abdollahzadeh, I. Belevich, E. Jokitalo, A. Sierra, J. Tohka
    Computer Methods and Programs in Biomedicine, 2022
  • Spatial statistics for understanding tissue organization
  • A. Behanova, A. Klemm, C. Wählby
    Frontiers in Physiology, 2022
  • The link between gliomas infiltration and white matter architecture investigated with electron microscopy and diffusion tensor imaging
  • F. Latini, M. Fahlström, A. Beháňová, I. Sintorn, M. Hodik, K. Staxäng, M. Ryttlefors
    NeuroImage Clinical, 2021
  • BV-2 microglial cells overexpressing C9orf72 hexanucleotide repeat expansion produce DPR proteins and show Normal functionality but no RNA foci
  • H. Rostalski, T. Hietanen, S. Leskelä, A. Behánová, A. Abdollahzadeh, R. Wittrahm, P. Mäkinen, N. Huber, D. Hoffmann, E. Solje, A.M. Remes, T. Natunen, M. Takalo, J. Tohka, M. Hiltunen, A. Haapasalo
    Frontiers in Neurology, 2020

    Skills & Proficiency

    Python

    Matlab

    Microsoft Office

    InkScape

    Programming language R

    MIT App Inventor

    Blender

    Ultimaker Cura

    LabVIEW 2016

    Maple