Multiscan 4D-STEM datasets on molecular crystals: biotin and Ni(dppf)Cl2

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 NCEM. 

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 custom 10 μm C2 aperture (Norcada) to access a range of narrow (<0.1 mrad) semiconvergence angles. Using a custom DigitalMicrograph script, multiscan 4D-STEM data were acquired with the 4D Camera operating at 87000 frames per second. As an illustrative example, each biotin dataset is comprised of 512×512 probe positions and 576×576 detector pixels, resulting in 174 GB of raw data per scan. These raw data were counted and reduced 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 HDF5 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 molecular crystal (25 for biotin, 300 for Ni(dppf)Cl2), alongside a sequence of simultaneously acquired HAADF images.

Experimental parameters for biotin:

Accelerating voltage
300 kV

Semiconvergence angle
0.07 mrad

Scan dimensions
512×512

Real-space step size
9.22 nm

Estimated probe size (FWHM)
14.4 nm

Total illuminated area
11.2 μm^2

Estimated fluence per probe position
0.15 e- Å^(-2)

Total size of raw data
4350 GB

Total size of sparsified data
2.18 GB

Experimental parameters for Ni(dppf)Cl2:

Accelerating voltage
200 kV

Semiconvergence angle
0.07 mrad

Scan dimensions
256×256

Real-space step size
15.1 nm

Estimated probe size (FWHM)
18.4 nm

Total illuminated area
7.55 μm^2

Estimated fluence per probe position
1.5 e- Å^(-2)

Total size of raw data
13200 GB

Total size of sparsified data
9.93 GB