Dataset Open Access

Structure Assisted Compressed Sensing Reconstruction of Undersampled AFM Images Dataset

Oxvig, Christian Schou; Arildsen, Thomas; Larsen, Torben


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  <identifier identifierType="DOI">10.5281/zenodo.18401</identifier>
  <creators>
    <creator>
      <creatorName>Oxvig, Christian Schou</creatorName>
      <givenName>Christian Schou</givenName>
      <familyName>Oxvig</familyName>
      <affiliation>Department of Electronic Systems, Aalborg University</affiliation>
    </creator>
    <creator>
      <creatorName>Arildsen, Thomas</creatorName>
      <givenName>Thomas</givenName>
      <familyName>Arildsen</familyName>
      <nameIdentifier nameIdentifierScheme="ORCID" schemeURI="http://orcid.org/">0000-0003-3254-3790</nameIdentifier>
      <affiliation>Department of Electronic Systems, Aalborg University</affiliation>
    </creator>
    <creator>
      <creatorName>Larsen, Torben</creatorName>
      <givenName>Torben</givenName>
      <familyName>Larsen</familyName>
      <affiliation>Department of Electronic Systems, Aalborg University</affiliation>
    </creator>
  </creators>
  <titles>
    <title>Structure Assisted Compressed Sensing Reconstruction of Undersampled AFM Images Dataset</title>
  </titles>
  <publisher>Zenodo</publisher>
  <publicationYear>2015</publicationYear>
  <subjects>
    <subject>Atomic Force Microscopy</subject>
    <subject>Compressed Sensing</subject>
    <subject>Undersampling</subject>
    <subject>Image Reconstruction</subject>
    <subject>Reproducible Research</subject>
  </subjects>
  <dates>
    <date dateType="Issued">2015-06-10</date>
  </dates>
  <resourceType resourceTypeGeneral="Dataset"/>
  <alternateIdentifiers>
    <alternateIdentifier alternateIdentifierType="url">https://sandbox.zenodo.org/record/18401</alternateIdentifier>
  </alternateIdentifiers>
  <relatedIdentifiers>
    <relatedIdentifier relatedIdentifierType="DOI" relationType="Cites">10.5281/zenodo.17573</relatedIdentifier>
    <relatedIdentifier relatedIdentifierType="DOI" relationType="IsPreviousVersionOf">10.5281/zenodo.60512</relatedIdentifier>
    <relatedIdentifier relatedIdentifierType="URL" relationType="IsPartOf">https://sandbox.zenodo.org/communities/zenodo</relatedIdentifier>
  </relatedIdentifiers>
  <rightsList>
    <rights rightsURI="http://creativecommons.org/licenses/by/4.0/legalcode">Creative Commons Attribution 4.0 International</rights>
    <rights rightsURI="info:eu-repo/semantics/openAccess">Open Access</rights>
  </rightsList>
  <descriptions>
    <description descriptionType="Abstract">&lt;p&gt;This deposition contains&amp;nbsp;the results from a simulation of reconstructions of undersampled atomic force microscopy (AFM) images. The reconstructions were obtained using weighted iterative thresholding compressed sensing algorithms.&lt;/p&gt;

&lt;p&gt;The&amp;nbsp;deposition&amp;nbsp;consists of:&lt;/p&gt;

&lt;ol&gt;
	&lt;li&gt;An &amp;nbsp;HDF5&amp;nbsp;database containing the results from&amp;nbsp;simulations of reconstructions of undersampled atomic force microscopy images (&lt;em&gt;weighted_it_reconstructions.hdf5&lt;/em&gt;).&lt;/li&gt;
	&lt;li&gt;The Python script which was used to create the database (&lt;em&gt;weighted_it_reconstructions.py&lt;/em&gt;).&lt;/li&gt;
	&lt;li&gt;MD5 and SHA256 checksums of the database and Python script files (&lt;em&gt;weighted_it_reconstructions.MD5SUMS /&amp;nbsp;weighted_it_reconstructions.SHA256SUMS&lt;/em&gt;).&lt;/li&gt;
&lt;/ol&gt;

&lt;p&gt;The HDF5 database is licensed under CC BY 4.0 (http://creativecommons.org/licenses/by/4.0/) . Since the CC BY 4.0 license is not well suited for source code,&amp;nbsp;the Python script is licensed under the BSD 2-Clause license (http://opensource.org/licenses/BSD-2-Clause) .&lt;/p&gt;

&lt;p&gt;&lt;strong&gt;The files are provided as-is with no warranty as detailed in the above mentioned licenses.&lt;/strong&gt;&lt;/p&gt;

&lt;p&gt;The database is split into four parts:&lt;/p&gt;

&lt;ol&gt;
	&lt;li&gt;weighted_it_reconstructions.hdf5.tar.xz.part-00&lt;/li&gt;
	&lt;li&gt;weighted_it_reconstructions.hdf5.tar.xz.part-01&lt;/li&gt;
	&lt;li&gt;weighted_it_reconstructions.hdf5.tar.xz.part-02&lt;/li&gt;
	&lt;li&gt;weighted_it_reconstructions.hdf5.tar.xz.part-03&lt;/li&gt;
&lt;/ol&gt;

&lt;p&gt;These four parts must be concatenated before the database&amp;nbsp;can be extracted from the&amp;nbsp;tar.xz archive. On Unix-like systems this may be done using:&lt;/p&gt;

&lt;p&gt;&lt;em&gt;cat weighted_it_reconstructions.hdf5.tar.xz.part-* &amp;gt;&amp;nbsp;weighted_it_reconstructions.hdf5.tar.xz&lt;/em&gt;&lt;/p&gt;

&lt;p&gt;after which&amp;nbsp;the archive may be extracted, e.g.,&amp;nbsp;using:&lt;/p&gt;

&lt;p&gt;&lt;em&gt;tar&amp;nbsp;xfJ&amp;nbsp;weighted_it_reconstructions.hdf5.tar.xz&lt;/em&gt;&lt;/p&gt;

&lt;p&gt;&lt;strong&gt;WARNING: The extracted HDF5 database has a size of 70 GiB.&lt;/strong&gt;&lt;/p&gt;

&lt;p&gt;The simulation results in the database are based on&amp;nbsp;&amp;quot;Atomic Force Microscopy Images of Cell Specimens&amp;quot; by Christian Rankl licensed under CC BY 4.0 (http://creativecommons.org/licenses/by/4.0/). The original images are available at http://dx.doi.org/10.5281/zenodo.17573. The&amp;nbsp;original images are provided as-is without warranty of any kind. Both&amp;nbsp;the original images as well as adapted images are part of the dataset.&amp;nbsp;&lt;/p&gt;</description>
  </descriptions>
</resource>
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