% [frameInfo imgDenoised] = detectSpotsWT(img, S, dthreshold, postProcLevel)
%
% Performs detection of local intensity clusters through a combination of
% multiscale products and denoising by iterative filtering from
% significant coefficients:
% Olivo-Marin, "Extraction of spots in biological images using multiscale products," Pattern Recoginition 35, pp. 1989-1996, 2002.
% Starck et al., "Image Processing and Data Analysis," Section 2.3.4, p. 73
%
% Parts of this function are based on code by Henry Jaqaman.
% Francois Aguet, March 2010
130| Appendices
imgDenoised = imgDenoised + resDenoised; % add significant residuals res = img - imgDenoised;
sigma_res1 = std(res(:));
delta = abs(sigma_res0/sigma_res1 - 1);
sigma_res0 = sigma_res1;
end
%===================================================
% Multiscale product of wavelet coefficients
%===================================================
% The support of the objects is given by the multiscale product in the wavelet domain.
mask = bwmorph(mask, 'spur'); % remove single pixels 8-attached to clusters mask = bwmorph(mask, 'spur');
Appendices |131
% Compute area and center of mass for each component
stats = regionprops(labels, imgDenoised, 'Area', 'WeightedCentroid', [yi,xi] = ind2sub([ny nx], stats(n).PixelIdxList);
[ym,xm] = ind2sub([ny nx], maxCoords(n).PixelIdxList);
area(n) = stats(n).Area;
elseif nMaxima(n)==0 % no maximum was detected for this cluster maxValueIdx = find(values == max(values));
xmax(n) = xi(maxValueIdx(1));
ymax(n) = yi(maxValueIdx(1));
nMaxima(n) = 1;
labelVect(n) = labels(ymax(n), xmax(n));
else % resolve multiple maxima cases
maxValues = localMax(sub2ind(size(localMax), ym, xm)); % highest local max maxIdx = find(maxValues == max(maxValues));
xmax(n) = xm(maxIdx(1));
ymax(n) = ym(maxIdx(1));
132| Appendices
Appendices |133
%=======================
% Subfunctions
%=======================
function result = significantCoefficientDenoising(img, S) mask = zeros(size(img));
result = zeros(size(img));
W = awt(img, S);
for s = 1:S
tmp = W(:,:,s);
mask(abs(tmp) >= 3*std(tmp(:))) = 1;
result = result + tmp.*mask;
end
134| Appendices
Acknowledgements
I would like to thank Prof. Dr. Reinhard Jahn not only for his invaluable support and guidance throughout this PhD project but also because he shares his enthusiasm and love for science with his students.
Many thanks go to Dr. Andrew Woehler for patiently helping me face the challenges and sustain my motivation. I would like to thank Andrew also for his constant support, scientific inputs and technical assistance throughout my PhD from the first steps of developing the assay to writing the manuscript and the thesis.
I would like to thank the members of my thesis committee Prof. Dr. Silvio O. Rizzoli, Prof.
Dr. Tobias Moser and Dr. Geert van den Bogaart for the discussion during the committee meetings and their helpful scientific inputs. I would like to express additional thanks to Geert for his great help with setting up the microscope in the beginning of my PhD and also for his feedback and criticism throughout writing this thesis. I also especially thank Vedran Vasic for carefully proofreading my PhD thesis.
I would like to express my gratitude to Prof. Dr. Venkatesh N. Murthy and Dr. William J.
Tyler for kindly sharing the transgenic mice with us, and also to Dr. Ulrike Teichmann, Sascha Krause and Thomas Gundlach for their help with animal delivery and taking care of the mice. I am grateful to my collaborators; Dr. Julia Preobraschenski, Dr. Dietmar Riedel, Dr.
Saheeb Ahmed and Dr. Lars Kastrup for their helpful scientific inputs and technical assistance. I would like to thank Dr. Gotfried Meiskes, Dr. Hans Dieter Schmitt and Elisa Reckmann-Heinrich for their help with lab-related issues. In addition, I thank Brigitte Barg-Kues and Sigrid Schmidt for their technical assistance, and Dr. Javier Matias Hernandez, Dr.
John Chua and Dr. Yongsoo Park for their scientific inputs.
I would like to thank all the past and present members of the Neurobiology department for providing a nice and friendly working atmosphere especially Partho, Angel, Dragomir and Beyenech.
I am especially grateful to Mahdokht Kohnasal Nodehi for her close friendship, scientific discussions and for her help with mass spectrometry, and also to Tahere and Sasha for their encouragements when the experiments were not working!
I am very thankful to all my friends in Göttingen, especially to Fatemeh, Elham, Ehsan, Mostafa, Mayur, Bekir, Diana, David, Chaitali, Vinita, Sünke and Alonso for the great time we had and for their support.
Lastly and most importantly, I would like to thank my family without whose support I would have not achieved any of my goals in my life and to whom I dedicate this thesis.
Curriculum Vitae |135
Curriculum Vitae
EDUCATION
Doctor of Philosophy
“Neuroscience”, Max-Planck Institute of Biophysical Chemistry, Göttingen, Germany.
Apr.2012-Nov.2015 Master of Science
“Neuroscience”, Max-Planck Institute for Experimental Medicine, Göttingen, Germany.
Oct. 2011-Mar. 2012.
“Cellular and Molecular Biology-Genetics”, Shahed University, Tehran, Iran.
Sep.2005 -Feb.2009.
RESEARCH EXPERIENCE
PhD Thesis: “A Single-Vesicle Assay to Study the Electrochemical Gradient Regulation in Glutamatergic and GABAergic Synaptic Vesicles”
2012-2015, Prof. Dr. Reinhard Jahn, Max-Planck Institute of Biophysical Chemistry, Göttingen, Germany.
Master’s Thesis: “Presynaptic Waveform Change and Neurotransmitter Release in Eag1 Knockout Mice”
2011-2012, Prof. Dr. Luis Pardo, Max Planck Institute for Experimental Medicine, Göttingen, Germany.
Master’s Thesis: “Investigation of the role of Arginine 97 in allosteric signal transduction pathway of Methylglyoxal Synthase”
2009-2011, Dr. Khosro Khajeh, Tarbiat Modares University, Tehran, Iran.
Research Intern.: “TheRole of the Linker Domain of Synaptobrevin in SNARE-Mediated Liposome Fusion”
2011, Prof. Dr. Reinhard Jahn, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany.
Research Intern.: “Electrophysiological characterization of cells in Neuroblastoma culture”
2011, Dr. Luis Pardo, Max Planck Institute for Experimental Medicine, Göttingen, Germany.
Research Intern.: “The role of HATs and HDACs in Schizophrenia and Aging”
2011, Dr. André Fischer, European Neuroscience Institue, Göttingen, Germany.
136| Curriculum Vitae
Summer Project: “In vitro effect of antidepressant drugs on murine Macrophages and Lymphocytes”
2009, Dr. Roya Yraei, Shahed University, Tehran, Iran.
Bachelor’s Thesis: “Biological Applications of Electrospun Nanofibers”
2009, Dr. Omid Ranaei Siadat, Shahed University, Tehran, Iran.
CONFERENCES
Horizons in Molecular Biology
Awarded student talk, ‘Regulation of neurotransmitter uptake into synaptic vesicles at the single vesicle level’, September 2015, Göttingen, Germany.
Gordon Research Conference on ‘Synaptic Transmission’
Selected Poster, ‘Regulation of neurotransmitter uptake into synaptic vesicles at the single vesicle level’
August 2014, New Hampshire, USA.
Biennial Neurizons Conference
Organizer, May 2013, Gottingen, Germany
FENS satellite event: “Vesicular transporters: old story, fresh look!”
July 2012, Barcelona, Spain.
The Second National Conference on “Biotechnology and its new applications”
Oral Presentation,“Tissue engineering and Electrospinning at Nanobiotechnology”.
October 2008, Alzahra University, Tehran, Iran.
10th International Congress of Immunology and Allergy
Poster, “In vitro effect of antidepressant drugs on murine macrophages and lymphocytes”.
May 2010, Tehran, Iran.
PRIZES AND AWARDS
Awarded poster, Horizons in Molecular Biology Symposium, 2015, Göttingen, Germany.
Awarded Student Talk, Horizons in Molecular Biology Symposium, 2015, Göttingen, Germany.
Awarded poster, Gordon Research Conference on ‘Synaptic Transmission’, 2015, New Hampshire, USA.
National Foundation of Elites stipend, 2009, Iran.
First Rank in 14𝑡ℎ Nationwide Student Olympiad in the field of Biology, July 2009, Tehran, Iran.
Curriculum Vitae |137 PUBLICATIONS
Zohreh Farsi, Julia Preobraschenski, Geert van den Bogaart, Dietmar Riedel, Reinhard Jahn, Andrew Woehler. “Single-vesicle imaging reveals different transport mechanisms between glutamatergic and GABAergic vesicles’, in preparation.
Lena Sünke Mortensen, Hartmut Schmidt, Zohreh Farsi, Alonso Barrantes-Freer, Roser Ufartes, Jens Eilers, Takeshi Sakaba, Walter Stühmer, and Luis A. Pardo. “KV10.1 potassium channels modulate presynaptic short-term plasticity at the parallel fibre - Purkinje cell synapse” The Journal of Physiology 593.1, 181-196 (2014).
Javier M. Hernandez, Alexander Stein, Elmar Behrmann, Dietmar Riedel, Anna Cypionka, Zohreh Farsi, Peter J.Walla, Stefan Raunser, Reinhard Jahn. “Membrane fusion intermediates via directional and full assembly of the SNARE complex” Science 22, 336 (2012).
Zohreh Farsi, Helmut Pein, Mohammad Pazhang, Shekoofeh Zareian, Seyed-Omid Ranaei-Siadat, Khosro Khajeh. “Conferral of allostery to Thermus sp. GH5 methylglyoxal synthase by a single mutation” The Journal of Biochemistry 152, 531-8 (2012).