Dataset Open Access

Three-dimensional subnanoscale imaging of unit cell doubling due to octahedral tilting and cation modulation in strained perovskite thin films

Nord, Magnus; Ross, Andrew; McGrouther, Damien; Barthel, Juri; Moreau, Magnus; Hallsteinsen, Ingrid; Tybell, Thomas; MacLaren, Ian

Transmission electron microscopy data used in the journal publication "Three-dimensional subnanoscale imaging of unit cell doubling due to octahedraltilting and cation modulation in strained perovskite thin films"

Data files

There are two data types:

  • Scanning TEM (STEM) diffraction patterns acquired with a Medipix3 detector (Merlin): m004_LSMO_LFO_STO_medipix.hdf5
  • Atomic resolution STEM data, both annular dark field (ADF) and annular bright field (ABF), which were acquired simultaneously: s007_ADF.hdf5, s007_ABF.hdf5

The data can be loaded in python using h5py.

For the Medipix3 data:

import h5py
f = h5py.File('m004_LSMO_LFO_STO_medipix.hdf5', mode='r')
data = f['fpd_expt/fpd_data/data']
data_subset = data[0:16, 0:16, :, :]

For the STEM-ADF or STEM-ABF data:

import h5py
f = h5py.File('s007_ADF.hdf5', mode='r')
data = f['Experiments/__unnamed__/data']

Exploring the Medipix3 dataset 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()

Loading the STEM-ADF or STEM-ABF data using HyperSpy, which automatically loads the probe scaling:

import hyperspy.api as hs
s = hs.load("s007_ADF.hdf5")
s.plot()


Processing files

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

  • d00N_...: Medipix3 data processing
  • a00N_...: Atomic resolution STEM-ADF and STEM-ABF processing using Atomap

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

 

Files (670.2 MB)
Name Size
a001_atomap_atom_lattice.zip
md5:f2af4d1294613ef017f9a86a536e6a92
44.3 MB Download
a001_make_atom_lattice.py
md5:226137c66a29fef8c376db9246bf15d4
555 Bytes Download
d001_get_radial_averaged_dataset.py
md5:067eab998dde92869fd9b3d05879ea2b
1.1 kB Download
d001_radial_integration.zip
md5:f6dbc599a93a0ae9e85d6594bceaaee9
19.1 MB Download
d002_get_holz_data_from_radial.py
md5:2b86dc6755f42b456d6e13fd5bb23665
3.7 kB Download
d002_processed.zip
md5:ffb4f992b1e3e17a7e09683900210f2e
5.8 MB Download
m004_LSMO_LFO_STO_medipix.hdf5
md5:6fa094a0e964deb4a6d5bf734bbf39ef
589.8 MB Download
run_all_scripts.py
md5:4613afe4e199a9720a854a158be46a9c
252 Bytes Download
s007_ABF.hdf5
md5:47056a1e1913909e9d502e83a9b911d7
5.5 MB Download
s007_ADF.hdf5
md5:18ac63c64a79af848f94bcb40d80795c
5.6 MB Download
34
11
views
downloads
All versions This version
Views 3434
Downloads 1111
Data volume 4.8 GB4.8 GB
Unique views 1919
Unique downloads 88

Share

Cite as