DOI: 10.5281/zenodo.18200831
title: Multiscan cryo-4D-STEM datasets on protein crystals: lysozyme and myoglobin

description: This repository contains data from scanning nanobeam electron diffraction experiments acquired using the 4D Camera installed on the double-aberration-corrected TEAM 0.5 instrument at the National Center for Electron Microscopy facility of the Molecular Foundry at Lawrence Berkeley National Laboratory. 

Before data acquisition, the incident beam current was reduced to the detection threshold of the fluorescent screen ammeter (<40 pA) by using the monochromator focus as a continuously adjustable gun lens. Beam flux was estimated from previous reference measurements using a Faraday cup and an ammeter under similar conditions.

A near-parallel probe was formed by using a 10 μm C2 aperture to access a 0.07 mrad semiconvergence angle. Using a custom DigitalMicrograph script, multiscan 4D-STEM data were acquired with the 4D Camera operating at 87000 frames per second. Raw images were compressed to a sparse, linear-index-encoded electron event representation (EER) in HDF5 format on the NERSC supercomputer, Perlmutter, using the open-source software package stempy. These sparse files can be interactively viewed using our open-source python-based software, DuSC Explorer.

Each directory contains a time series of several consecutive 4D-STEM scans acquired on the same triclinic lysozyme or monoclinic myoglobin microcrystal, alongside a sequence of simultaneously acquired HAADF-STEM images. These experiments were conducted either at room temperature (labeled as “rt”) or on samples plunge-frozen in liquid ethane, cryo-transferred into the microscope under inert atmosphere, and held at ~85 K throughout the experiment (labeled as “cryo”).

Experimental parameters

Note: to accurately identify the datasets based on their HAADF-STEM images, refer to the labels.png file in the repository.

cryo lysozyme (1)




Accelerating voltage
300 kV


Semiconvergence angle
0.07 mrad


Scan dimensions
512 x 512


Real-space step size
4.6 nm


Estimated probe size (FWHM)
15 nm


Total illuminated area
5.6 um^2


Estimated fluence per probe position
0.6 e/A^2


Total size of raw data
2268 GB


Total size of sparsified data
14.7 GB




cryo lysozyme (2)




Accelerating voltage
300 kV


Semiconvergence angle
0.07 mrad


Scan dimensions
512 x 512


Real-space step size
4.6 nm


Estimated probe size (FWHM)
15 nm


Total illuminated area
5.6 um^2


Estimated fluence per probe position
0.6 e/A^2


Total size of raw data
2430 GB


Total size of sparsified data
14.7 GB




rt lysozyme




Accelerating voltage
300 kV


Semiconvergence angle
0.07 mrad


Scan dimensions
512 x 512


Real-space step size
4.6 nm


Estimated probe size (FWHM)
15 nm


Total illuminated area
5.6 um^2


Estimated fluence per probe position
0.4 e/A^2


Total size of raw data
1620 GB


Total size of sparsified data
2.36 GB




cryo myoglobin




Accelerating voltage
300 kV


Semiconvergence angle
0.07 mrad


Scan dimensions
512 x 512


Real-space step size
4.6 nm


Estimated probe size (FWHM)
15 nm


Total illuminated area
5.6 um^2


Estimated fluence per probe position
0.6 e/A^2


Total size of raw data
810 GB


Total size of sparsified data
2.05 GB