Dataset Open Access
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"
There are two data types:
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()
All the TEM data has been processed using python scripts, which is named based on the type of processing:
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