Dataset Open Access

Structure Assisted Compressed Sensing Reconstruction of Undersampled AFM Images Dataset

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

This deposition contains 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.

The deposition consists of:

  1. An  HDF5 database containing the results from simulations of reconstructions of undersampled atomic force microscopy images (weighted_it_reconstructions.hdf5).
  2. The Python script which was used to create the database (weighted_it_reconstructions.py).
  3. MD5 and SHA256 checksums of the database and Python script files (weighted_it_reconstructions.MD5SUMS / weighted_it_reconstructions.SHA256SUMS).

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, the Python script is licensed under the BSD 2-Clause license (http://opensource.org/licenses/BSD-2-Clause) .

The files are provided as-is with no warranty as detailed in the above mentioned licenses.

The database is split into four parts:

  1. weighted_it_reconstructions.hdf5.tar.xz.part-00
  2. weighted_it_reconstructions.hdf5.tar.xz.part-01
  3. weighted_it_reconstructions.hdf5.tar.xz.part-02
  4. weighted_it_reconstructions.hdf5.tar.xz.part-03

These four parts must be concatenated before the database can be extracted from the tar.xz archive. On Unix-like systems this may be done using:

cat weighted_it_reconstructions.hdf5.tar.xz.part-* > weighted_it_reconstructions.hdf5.tar.xz

after which the archive may be extracted, e.g., using:

tar xfJ weighted_it_reconstructions.hdf5.tar.xz

WARNING: The extracted HDF5 database has a size of 70 GiB.

The simulation results in the database are based on "Atomic Force Microscopy Images of Cell Specimens" 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 original images are provided as-is without warranty of any kind. Both the original images as well as adapted images are part of the dataset. 

Files (8.1 GB)
Name Size
weighted_it_reconstructions.hdf5.tar.xz.part-00
md5:0c61117cc32605e48ead1522a1942d7b
2.1 GB Download
weighted_it_reconstructions.hdf5.tar.xz.part-01
md5:98b0007945892dbce179b97f7b00fcbc
2.1 GB Download
weighted_it_reconstructions.hdf5.tar.xz.part-02
md5:ef202a17721f7c644705c1e009376df3
2.1 GB Download
weighted_it_reconstructions.hdf5.tar.xz.part-03
md5:3dddf2b524a304fac97b1247424c966e
1.6 GB Download
weighted_it_reconstructions.MD5SUMS
md5:28fd10e109f68e1875ebcc7ce7559776
393 Bytes Download
weighted_it_reconstructions.py
md5:276dfd3d124e612cd0cd4a1c00afc1f1
19.0 kB Download
weighted_it_reconstructions.SHA256SUMS
md5:d07711fb46bc13db26aeeb3d639f878e
553 Bytes Download

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