Dataset Open Access

Strain Anisotropy and Magnetic Domains in Embedded Nanomagnets

Nord, Magnus; Semisalova, Anna; Kákay, Attila; Hlawacek, Gregor; MacLaren, Ian; Liersch, Vico; Volkov, Oleksii M.; Makarov, Denys; Paterson, Gary W.; Potzger, Kay; Lindner, Jürgen; Fassbender, Jürgen; McGrouther, Damien; Bali, Rantej

Transmission electron microscopy data and processing scripts related to the journal article "Strain Anisotropy and Magnetic Domains in Embedded Nanomagnets": https://doi.org/10.1002/smll.201904738

Data files

The data is contained within the 00N_....hdf5 files, which can be accessed using an HDF5 reader. Note that these datasets are very large, and trying to load one of them directly will most likely lead to your computer crashing.

Loading the data in python with h5py:

import h5py
f = h5py.File('003_stripe1.hdf5', mode='r')
data = f['fpd_expt/fpd_data/data']
data_subset = data[0:16, 0:16, :, :]

Exploring the datasets lazily, i.e. without loading the whole dataset into memory at the same time. Using pixStem:

import pixstem.api as ps
s = ps.load_ps_signal("003_stripe1.hdf5", lazy=True)
s.plot()


Processing files

All the TEM data has been processed using python scripts, which is named based on the type of processing:

  • d00N_...: STEM-DPC processing
  • l00N_...: lattice size processing
  • s00N_...: rotation "simulations" to find the relation between the scan and detector rotation

Several of the scripts generate intermediate files, which are saved in folders with the same prefix as the scripts. So the d001_... script makes a folder named d001_... . These intermediate files are included here as zip-files, since Zenodo doesn't support folder structures.

The python libraries required to run the scripts are listed in requirements.txt. Newer versions of the libraries will most likely also work.

To setup the python environment with the required libraries, and run all the scripts:

pip3 install -r requirements.txt
python3 run_all_scripts.py

This will most likely take several hours to complete.

Files (55.8 GB)
Name Size
003_stripe1.hdf5
md5:9c291128ccf1b81aa3ca72d9827a3b2b
6.2 GB Download
004_stripe2.hdf5
md5:b5831f8ca3b7ebff17c3f8a38b37fdac
5.5 GB Download
005_stripe3.hdf5
md5:c470817205cddb5f3325fcb84da69e9c
5.0 GB Download
006_stripe4.hdf5
md5:8b00389aba4d5b01068946ac512d4ba0
5.5 GB Download
007_stripe5.hdf5
md5:87bc09ccc6fb46e73ef793c257f737d8
5.5 GB Download
008_stripe6.hdf5
md5:d53496063590bfec67737f79d7ffc4bb
4.1 GB Download
009_stripe7.hdf5
md5:a99441e93c4520424ca31c2982b2d3a7
3.6 GB Download
010_stripe8.hdf5
md5:962a0ae61d8355d3c04304e4cf8dd18b
3.5 GB Download
013_overview1.hdf5
md5:cd444fcd0334697c902ba174d382dd76
4.4 GB Download
015_spiral_large_512x512.hdf5
md5:cd879751f24a6cb3d545043453a82513
12.2 GB Download
d001_dpc_raw.zip
md5:62a8e4ce66c5ad80c06a5e9b20d9762a
14.5 MB Download
d001_get_dpc_raw_signal.py
md5:9dd474f9edb4235a7ea335edc1c23d4c
3.0 kB Download
d002_dpc_cor.zip
md5:14d84e7edbbd308665cbd1593fd696bc
18.9 MB Download
d002_get_dpc_corrected_signal.py
md5:ddb5bbbd915d2280991cf74bc0a69b5d
4.0 kB Download
d003_dpc_raw_plot.zip
md5:c26c4be8e4553488391dd3f58935fd71
1.1 MB Download
d003_plot_dpc_raw_signal.py
md5:604a1b0047484cf35721c4ac5c8767e7
503 Bytes Download
d004_dpc_cor_plot.zip
md5:188ed99ac411b7e4c2b70803a66a409a
1.8 MB Download
d004_plot_dpc_cor_signal.py
md5:eb9c4364555fc0a2d8b903b5cda5ff8f
1.6 kB Download
d005_magnetic_domain_information.zip
md5:5a2c776f10250ff969e368312a9dcf53
5.3 MB Download
d005_plot_domain_stripe_visualization.py
md5:3a6cb6cdb039e055a247034d05e163b2
5.1 kB Download
d006_dpc_raw_spiral.zip
md5:6f2766f7cfe3b4841d178fb2c39b45ef
3.1 MB Download
d006_get_spiral_dpc_raw_signal.py
md5:10e843ddbdb3f4aa827f9747a6eb538e
2.4 kB Download
d007_dpc_cor_spiral.zip
md5:c998082fcb6f548cd81ccd64d201b25b
3.9 MB Download
d007_get_spiral_dpc_cor_signal.py
md5:a3e1c4a22f06688063bfe8d57252343a
2.0 kB Download
d008_make_overview_data_dpc_corr.py
md5:d0c22866cc52ab3e5b7b0e5918e279f9
1.8 kB Download
d008_overview_data_dpc_corr.zip
md5:6d7457edbaedffaf2676ed732145858b
2.1 MB Download
l001_get_diff_stripe_line_profiles.py
md5:c9663e90d46e88f42e0a4c9fd1457f16
6.1 kB Download
l001_line_profile_diff.zip
md5:e781d41e169c9b0ac76912cdc0a5b810
403.0 MB Download
l002_get_diff_overview_line_profile.py
md5:9287f0514a308770e1a176193f2ffeca
3.6 kB Download
l003_ellipse_data.zip
md5:80501eb7198e730d0aac8749d07aa2bd
44.4 kB Download
l003_get_ellipse_data.py
md5:9b43c997da6102a921443985251703df
2.1 kB Download
l004_ellipse_debug_plots.zip
md5:62c4499d074ad9a52d4090f4c2431424
1.5 MB Download
l004_plot_ellipse_data_debug.py
md5:d9d616cac9714b4c0ff862109481d3ed
2.9 kB Download
l005_get_lattice_parameter_stripes.py
md5:bc4f1c962ee6be6c41c433bff070efa6
3.8 kB Download
l005_lattice_size.zip
md5:9f4e8d12a46dc705cc14759ec7f654b6
34.7 kB Download
l006_get_stripe_lattice_parameter_and_errors.py
md5:fa8faa1bca1c7273cb8914974bc6b176
8.7 kB Download
l006_stripe_lattice_size_and_errors.zip
md5:0e4197bba1c358b1532c30e09478f156
689.0 kB Download
requirements.txt
md5:fa854ffce9374070e6906939c7ecd898
120 Bytes Download
run_all_scripts.py
md5:f59924bedd1e6c112640c742433efa47
1.6 kB Download
s001_make_simulated_dpc_signal.py
md5:14a486132a2f9d8b2885956542fa76e6
1.1 kB Download
s001_simulated_dpc_signal.zip
md5:29dc1911db439b5a7e7eada6a985efac
246.5 kB Download
s002_get_stripe_line_profiles.py
md5:a7b6462cb803f2a2cd29f9a290b045f8
7.7 kB Download
s002_line_profiles.zip
md5:7cb181d7bc17c88e6fa85be381e57dcb
41.1 MB Download
s003_make_simulated_lattice_dataset.py
md5:e338d4db8be81132cc35eccb200a5849
2.2 kB Download
s003_simulated_lattice_dataset.zip
md5:3fdef0309489c0f006de3ecac1f857a6
4.3 MB Download
s004_get_ellipse_data.zip
md5:20481baced8e406cc7898a94413d0458
6.0 kB Download
s004_get_stripe_simulated_ellipse_data.py
md5:303c1ffc1691b65ab044dbd73439ce66
2.2 kB Download
s005_plot_ellipse_simulated_data.py
md5:8e8d2d31c2941933ebd7919460224af9
2.0 kB Download
s005_simulated_ellipse_figures.zip
md5:b57f36e63e43ff4e7b99fe7a8b37ed6a
67.1 kB Download
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