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 (
  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 ( . 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 ( .

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 ( The original images are available at 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 md5:276dfd3d124e612cd0cd4a1c00afc1f1 19.0 kB Download
weighted_it_reconstructions.SHA256SUMS md5:d07711fb46bc13db26aeeb3d639f878e 553 Bytes Download


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