• Chip-based multimodal super-resolution microscopy for histological investigations of cryopreserved tissue sections 

      Villegas, Luis; Dubey, Vishesh Kumar; Nystad, Mona; Tinguely, Jean-Claude; Coucheron, David Andre; Dullo, Firehun Tsige; Priyadarshi, Anish; Acuna Maldonado, Sebastian Andres; Ahmad, Azeem; Mateos, Jose M.; Barmettler, Gery; Ziegler, Urs; Birgisdottir, Åsa Birna; Hovd, Aud-Malin Karlsson; Fenton, Kristin Andreassen; Acharya, Ganesh; Agarwal, Krishna; Ahluwalia, Balpreet Singh (Journal article; Tidsskriftartikkel; Peer reviewed, 2022-02-24)
      Histology involves the observation of structural features in tissues using a microscope. While diffraction-limited optical microscopes are commonly used in histological investigations, their resolving capabilities are insufficient to visualize details at subcellular level. Although a novel set of super-resolution optical microscopy techniques can fulfill the resolution demands in such cases, the ...
    • Learning nanoscale motion patterns of vesicles in living cells 

      Sekh, Arif Ahmed; Opstad, Ida Sundvor; Birgisdottir, Åsa Birna; Myrmel, Truls; Ahluwalia, Balpreet Singh; Agarwal, Krishna; Prasad, Dilip K. (Chapter; Bokkapittel, 2020)
      Detecting and analyzing nanoscale motion patterns of vesicles, smaller than the microscope resolution (~250 nm), inside living biological cells is a challenging problem. State-of-the-art CV approaches based on detection, tracking, optical flow or deep learning perform poorly for this problem. We propose an integrative approach, built upon physics based simulations, nanoscopy algorithms, and shallow ...
    • Members of the autophagy class III phosphatidylinositol 3-kinase complex I interact with GABARAP and GABARAPL1 via LIR motifs 

      Birgisdottir, Åsa Birna; Mouilleron, Stephane; Bhujabal, Zambarlal; Wirth, Martina; Sjøttem, Eva; Evjen, Gry; Zhang, Wenxin; Lee, Rebecca; O'Reilly, Nicola; Tooze, Sharon A; Lamark, Trond; Johansen, Terje (Journal article; Tidsskriftartikkel; Peer reviewed, 2019-03-04)
      Autophagosome formation depends on a carefully orchestrated interplay between membrane-associated protein complexes. Initiation of macroautophagy/autophagy is mediated by the ULK1 (unc-51 like autophagy activating kinase 1) protein kinase complex and the autophagy-specific class III phosphatidylinositol 3-kinase complex I (PtdIns3K-C1). The latter contains PIK3C3/VPS34, PIK3R4/VPS15, BECN1/Beclin 1 ...
    • Mitochondrial dynamics and quantification of mitochondria-derived vesicles in cardiomyoblasts using structured illumination microscopy 

      Opstad, Ida S.; Godtliebsen, Gustav; Ahluwalia, Balpreet Singh; Myrmel, Truls; Agarwal, Krishna; Birgisdottir, Åsa Birna (Journal article; Tidsskriftartikkel; Peer reviewed, 2021-11-12)
      Mitochondria are essential energy-providing organelles of particular importance in energy-demanding tissue such as the heart. The production of mitochondria-derived vesicles (MDVs) is a cellular mechanism by which cells ensure a healthy pool of mitochondria. These vesicles are small and fast-moving objects not easily captured by imaging. In this work, we have tested the ability of the optical ...
    • Multifocus microscopy with optically sectioned axial superresolution 

      Ströhl, Florian; Hansen, Daniel Henry; Nager Grifo, Mireia; Birgisdottir, Åsa Birna (Journal article; Tidsskriftartikkel, 2022)
      Multifocus microscopy enables recording of entire volumes in a single camera exposure. In dense samples, multifocus microscopy is severely hampered by background haze. Here, we introduce a scalable multifocus method that incorporates optical sectioning and offers axial superresolution capabilities. In our method, a dithered oblique light-sheet scans the sample volume during a single exposure, while ...
    • Physics-based machine learning for subcellular segmentation in living cells 

      Sekh, Arif Ahmed; Opstad, Ida Sundvor; Godtliebsen, Gustav; Birgisdottir, Åsa Birna; Ahluwalia, Balpreet Singh; Agarwal, Krishna; Prasad, Dilip K. (Journal article; Tidsskriftartikkel; Peer reviewed, 2021-12-15)
      Segmenting subcellular structures in living cells from fluorescence microscope images is a ground truth (GT)-deficient problem. The microscopes’ three-dimensional blurring function, finite optical resolution due to light diffraction, finite pixel resolution and the complex morphological manifestations of the structures all contribute to GT-hardness. Unsupervised segmentation approaches are quite ...
    • Site-specific reverse splicing of a HEG-containing group I intron in ribosomal RNA 

      Birgisdottir, Åsa Birna; Johansen, Steinar (Journal article; Tidsskriftartikkel; Peer reviewed, 2005)
      The myxomycete Didymium iridis (isolate Panama 2) contains a mobile group I intron named Dir.S956-1 after position 956 in the nuclear small subunit (SSU) rRNA gene. The intron is efficiently spread through homing by the intron-encoded homing endonuclease I-DirI. Homing endonuclease genes (HEGs) usually spread with their associated introns as a unit, but infrequently also spread independent ...