Ondrej Mandula PhD

Ondrej Mandula


Publications:
2014
  Localisation microscopy with quantum dots using non-negative matrix factorisation
Mandula, O, Sestak, IS, Heintzmann, R & Williams, CKI 2014, 'Localisation microscopy with quantum dots using non-negative matrix factorisation' Optics Express, vol 22, no. 20, pp. 24594-24605. DOI: 10.1364/OE.22.024594
We propose non-negative matrix factorisation with iterative restarts (iNMF) to model a noisy dataset of highly overlapping fluorophores with intermittent intensities. We can recover high-resolution images of individual sources from the optimised model, despite their high mutual overlap in the original data. Each source can have an arbitrary, unknown shape of the PSF and blinking behaviour. This allows us to use quantum dots as bright and stable fluorophores for localisation microscopy. We compare the iNMF results to CSSTORM, 3B and bSOFI. iNMF shows superior performance in the challenging task of super-resolution imaging using quantum dots. We can also retrieve axial localisation of the sources from the shape of the recovered PSF.
General Information
Organisations: Institute for Adaptive and Neural Computation .
Authors: Mandula, Ondrej, Sestak, Ivana Sumanovac, Heintzmann, Rainer & Williams, Christopher K. I..
Number of pages: 12
Pages: 24594-24605
Publication Date: 6 Oct 2014
Publication Information
Category: Article
Journal: Optics Express
Volume: 22
Issue number: 20
ISSN: 1094-4087
Original Language: English
DOIs: 10.1364/OE.22.024594
2012
  Line scan - structured illumination microscopy super-resolution imaging in thick fluorescent samples
Mandula, O, Kielhorn, M, Wicker, K, Krampert, G, Kleppe, I & Heintzmann, R 2012, 'Line scan - structured illumination microscopy super-resolution imaging in thick fluorescent samples' Optics Express, vol 20, no. 22, pp. 24167. DOI: 10.1364/OE.20.024167
Structured illumination microscopy in thick fluorescent samples is a challenging task. The out-of-focus fluorescence background deteriorates the illumination pattern and the reconstructed images suffer from influence of noise. We present a combination of structured illumination microscopy with line scanning. This technique reduces the out-of-focus fluorescence background, which improves the modulation and the quality of the illumination pattern and therefore facilitates the reconstruction. We present super-resolution, optically sectioned images of a thick fluorescent sample, revealing details of the specimen’s inner structure.
General Information
Organisations: Neuroinformatics DTC.
Authors: Mandula, Ondrej, Kielhorn, Martin, Wicker, Kai, Krampert, Gerhard, Kleppe, Ingo & Heintzmann, Rainer.
Pages: 24167
Publication Date: 22 Oct 2012
Publication Information
Category: Article
Journal: Optics Express
Volume: 20
Issue number: 22
ISSN: 1094-4087
Original Language: English
DOIs: 10.1364/OE.20.024167
  Line Scan - Structured Illumination Microscopy High-resolution imaging in thick fluorescent samples
Mandula, O & Heintzmann, R 2012, 'Line Scan - Structured Illumination Microscopy High-resolution imaging in thick fluorescent samples'.
General Information
Organisations: Neuroinformatics DTC.
Authors: Mandula, Ondrej & Heintzmann, Rainer.
Publication Date: 2012
Publication Information
Category: Poster
Original Language: English
2010
  Localisation microscopy using quantum dots
Mandula, O, Williams, CKI & Heintzmann, R 2010, 'Localisation microscopy using quantum dots' 40th Society for Neuroscience Annual Meeting, San Diego, United States, 13/11/10 - 17/11/10, .
Localisation microscopy (LM) techniques such as STORM/fPALM have proved to be viable techniques in biological research. These techniques provide super-resolution images of fluorescently labelled biological samples by localisation of
individual fluorophores. LM techniques become increasingly popular choice for
investigation of detailed structure of biological samples because of their
inexpensive realisation. We are working on an LM related technique using quantum dots (QD) as fluorescent markers. Quantum dots - with an order of magnitude higher brightness then organic fluorophores, exceptional photostability and non-toxicity - seem to be ideal fluorophores for fluorescence microscopy study of biological samples. Under a constant illumination, QD exhibit stochastic blinking in emission of fluorescent light. We use the fluorescence intermittency to separate individual overlapping QD within a diffraction limited volume. This makes the precise localisation of individual QD possible, and sub-resolution structure of the sample can be revealed. We record a time stack of wide field images of the sample stained with blinking QDs. To separate individual sources (QDs) we use a model based on non-negative matrix factorisation (NMF). Our NMF algorithm is a natural model for data corrupted with Poisson noise (such as microscopic images) using Czisar's I-divergence as a cost function. NMF based methods do not require knowledge about the point spread function (PSF) which makes it possible to use for 3D samples where fluorophores can be above or below the plane of focus or can be corrupted with various aberrations changing the shape of PSF across the field of view. We hope the method can significantly speed up the acquisition time for LM techniques, as well as make the use of QD possible for super-resolution fluorescence
General Information
Organisations: Institute for Adaptive and Neural Computation .
Authors: Mandula, Ondrej, Williams, Christopher K. I. & Heintzmann, Rainer.
Publication Date: 2010
Publication Information
Category: Poster
Original Language: English
  t-SNARE Protein Conformations Patterned by the Lipid Microenvironment
Rickman, C, Medine, CN, Dun, AR, Moulton, DJ, Mandula, O, Halemani, ND, Rizzoli, SO, Chamberlain, LH & Duncan, RR 2010, 't-SNARE Protein Conformations Patterned by the Lipid Microenvironment' Journal of Biological Chemistry, vol 285, no. 18, pp. 13535-13541. DOI: 10.1074/jbc.M109.091058

The spatial distribution of the target (t-) SNARE proteins (syntaxin and SNAP-25) on the plasma membrane has been extensively characterized. However, the protein conformations and interactions of the two t-SNAREs in situ remain poorly defined. By using super-resolution optical techniques and fluorescence lifetime imaging microscopy, we observed that within the t-SNARE clusters syntaxin and SNAP-25 molecules interact, forming two distinct conformations of the t-SNARE binary intermediate. These are spatially segregated on the plasma membrane with each cluster exhibiting predominantly one of the two conformations, representing the two-and three-helical forms previously observed in vitro. We sought to explain why these two t-SNARE intermediate conformations exist in spatially distinct clusters on the plasma membrane. By disrupting plasma membrane lipid order, we found that all of the t-SNARE clusters now adopted a single conformational state corresponding to the three helical t-SNARE intermediates. Together, our results define spatially distinct t-SNARE intermediate states on the plasma membrane and how the conformation adopted can be patterned by the underlying lipid environment.


General Information
Organisations: Deanery of Biomedical Sciences.
Authors: Rickman, Colin, Medine, Claire N., Dun, Alison R., Moulton, David J., Mandula, Ondrej, Halemani, Nagaraj D., Rizzoli, Silvio O., Chamberlain, Luke H. & Duncan, Rory R..
Keywords: (, , . )
Number of pages: 7
Pages: 13535-13541
Publication Date: 30 Apr 2010
Publication Information
Category: Article
Journal: Journal of Biological Chemistry
Volume: 285
Issue number: 18
ISSN: 0021-9258
Original Language: English
DOIs: 10.1074/jbc.M109.091058

Projects:
Localization microscopy using quantum dots (PhD)