January 12, 2024 Dataset Open Access

Li, Rui; Della Maggiora Valdes, Gabriel Eugenio; Andriasyan, Vardan; Petkidis, Anthony; Yushkevich, Artsemi; Kudryashev, Mikhail; Yakimovich, Artur

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    <subfield code="a">Li, Rui</subfield>
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    <subfield code="a">Della Maggiora Valdes, Gabriel Eugenio</subfield>
    <subfield code="u">Center for Advanced Systems Understanding (CASUS), Görlitz, Germany; Helmholtz-Zentrum Dresden-Rossendorf e. V. (HZDR), Dresden, Germany</subfield>
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    <subfield code="a">Andriasyan, Vardan</subfield>
    <subfield code="u">Department of Molecular Life Sciences, University of Zurich, Zurich, Switzerland</subfield>
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    <subfield code="a">Petkidis, Anthony</subfield>
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    <subfield code="a">Yushkevich, Artsemi</subfield>
    <subfield code="u">Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany</subfield>
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    <subfield code="a">Kudryashev, Mikhail</subfield>
    <subfield code="u">Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany; Institute of Medical Physics and Biophysics, Charite-Universitätsmedizin, Berlin, Germany</subfield>
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    <subfield code="a">Yakimovich, Artur</subfield>
    <subfield code="u">Center for Advanced Systems Understanding (CASUS), Görlitz, Germany; Helmholtz-Zentrum Dresden-Rossendorf e. V. (HZDR), Dresden, Germany; Artificial Intelligence for Life Sciences CIC, London, United Kingdom; nstitute of Computer Science, University of Wrocław, Wrocław, Poland</subfield>
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    <subfield code="a">&lt;p&gt;&lt;strong&gt;Dataset&lt;/strong&gt;&lt;/p&gt;

&lt;p&gt;This dataset contains a sample of 600 fluorescently labelled nuclei of cultured cells imaged using widefield fluorescence microscopy and confocal fluorescence microscopy at different focal planes.&lt;/p&gt;



&lt;p&gt;Image preprocessing&lt;/p&gt;

&lt;p&gt;Notably, the hardware precision of the sectioning process led to variations in the step size when shifting the focal plane between the two devices. This resulted in distinct z-dimensions between the datasets obtained from the two microscopy techniques. The confocal stacks in raw data comprised 92 focal planes, whereas the widefield stacks consisted of only 40 slices. Each focal plane image had a shape [2048, 2048, 1]. Assuming the central slice of each stack to be the in-focus, we performed z-direction registration by downsampling the confocal stacks from the central slice (46th) to match the 40 slices of the widefield stacks. Due to the instrumental limitations, a slight drift was noticeable between images. To address this, we used the phase cross-correlation algorithm [2] to compensate for the offsets on the x-y plane for the z-dimension registered image stacks. Having completed the registration and alignment along three dimensions, we then partitioned the original images into non-overlapping patches with dimensions of [128, 128, 1] in the xy plane. This partitioned dataset serves as the test dataset for validating our blind-deconvolution model, conducted without the specific Point Spread Function (PSF) parameters [3].&lt;/p&gt;



&lt;p&gt;&lt;strong&gt;Files description&lt;/strong&gt;&lt;/p&gt;

&lt;p&gt;The Widefield-confocal Microscopy Dataset is stored in the &amp;#39;*.npz&amp;#39; format, encompassing the variables &amp;#39;c_img&amp;#39; and &amp;#39;w_img.&amp;#39; These handles respectively denote the confocal images and their corresponding widefield microscopy images. Both types of data undergo registration, alignment, and normalization, with values scaled to range between [0.0, 1.0]. For each category, the data has a shape of [600, 128, 128, 40], where the first dimension denotes the individual field of view and the last dimension signifies the z-dimension representing changes in the focal plane for virtual sectioning. The first dimension corresponds to the patch number, each with a patch size of [128, 128].&lt;/p&gt;

&lt;p&gt;&lt;strong&gt;&amp;nbsp;&lt;/strong&gt;&lt;/p&gt;



&lt;p&gt;&lt;strong&gt;Sample preparation and microscopy&lt;/strong&gt;&lt;/p&gt;

&lt;p&gt;A549 lung carcinoma cell line cells were seeded in 96-well imaging plates a night prior to imaging, then fixed with 4% paraformaldehyde (Sigma) and stained for DNA with Hoechst 33342 fluorescent dye (Sigma). Cell culture was maintained similarly to the procedures described in [1]. Next, stained cell nuclei were imaged using ImageXpress Confocal system (Molecular Devices) in either confocal or widefield mode employing Nikon 20X Plan Apo Lambda objective. To obtain 3D information images in both modes were acquired as Z-stacks with 0.3 &amp;micro;m and 0.7 &amp;micro;m for confocal and widefield modes respectively. Confocal z-stack was Nyquist sampled. The excitation wavelength was 405 nm and the emission was 452 nm. Using these settings, we obtained&amp;nbsp;individual stacks for both modalities, with each stack covering 2048 by 2048 pixels or 699 by 699 &amp;micro;m.&lt;/p&gt;



&lt;p&gt;&lt;strong&gt;References&lt;/strong&gt;&lt;/p&gt;

&lt;ol&gt;
	&lt;li&gt;
	&lt;p&gt;Yakimovich, Artur, et al. &amp;quot;Plaque2. 0&amp;mdash;a high-throughput analysis framework to score virus-cell transmission and clonal cell expansion.&amp;quot; PloS one 10.9 (2015): e0138760.&lt;/p&gt;
	&lt;/li&gt;
	&lt;li&gt;
	&lt;p&gt;Alink, Mark S. Oude, et al. &amp;quot;Lowering the SNR wall for energy detection using cross-correlation.&amp;quot; IEEE transactions on vehicular technology 60.8 (2011): 3748-3757.&lt;/p&gt;
	&lt;/li&gt;
	&lt;li&gt;
	&lt;p&gt;Li, Rui, et al. &amp;quot;Microscopy image reconstruction with physics-informed denoising diffusion probabilistic model.&amp;quot; arXiv preprint arXiv:2306.02929 (2023).&lt;/p&gt;
	&lt;/li&gt;
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