Data and code available at

NSSM

This repository contains example code and data accompanying the paper: "Nonlinear sound-sheet microscopy: imaging opaque organs at the capillary and cellular scale".

NSSM Verasonics Imaging Sequence

The file NSSM_Sequence.m contains a Verasonics imaging sequence that allows volumetric nonlinear sound-sheet microscopy (NSSM).

While running the sequence, two orthogonal sound sheets will be displayed, and the active displayed sound sheet can be changed using a slider in the VSX GUI.

After running the sequence, the full volume can be reconstructed using the script NSSM_Sequence_Postprocess.m. This will reconstruct all acquired sound sheets, and compound the two arrays.

Example Data

Example datasets are available on Zenodo: 10.5281/zenodo.14740878. Download the .mat files from Zenodo and store them in the data folder.

File	Content
RFData_planes_figure_2E.mat	RF data of two orthogonal sound sheets imaging GV Wells with E. Coli. Process with demo_reconstruct_orthogonal_NSSM_images.m.
beamformed_volume_figure_2E.mat	Reconstructed 3D images of GV Wells with E. Coli. View with demo_navigate_3D_NSSM_data.m.
RFData_planes_figure_3B.mat	RF data of two orthogonal sound sheets imaging mARG expression in orthopic tumors. Process with demo_reconstruct_orthogonal_NSSM_images.m.
beamformed_volume_figure_3B.mat	Reconstructed 3D images of mARG expression in orthopic tumors. View with demo_navigate_3D_NSSM_data.m.

Wells with E. Coli

Representative dataset for paper figure 2D,E. The file RFData_planes_figure_2E.mat contains the RFData and the required parameters to reconstruct two orthogonal sound sheets, in SSM and NSSM mode. The file demo_reconstruct_orthogonal_NSSM_images.m shows how to reconstruct the sound sheet data.

The file beamformed_volume_figure_2E.mat contains beamformed SSM and NSSM volumes as displayed in figure 2G. Use demo_navigate_3D_NSSM_data.m to view the volumes.

mARG expression in orthopic tumors

Representative dataset for paper figure 3B. The file RFData_planes_figure_3B.mat contains the RFData and the required parameters to reconstruct two orthogonal sound sheets, in SSM and NSSM mode. The file demo_reconstruct_orthogonal_NSSM_images.m shows how to reconstruct the sound sheet data.

The file beamformed_volume_figure_3B.mat contains beamformed SSM and NSSM volumes as displayed in figure 3C. Use demo_navigate_3D_NSSM_data.m to view the volumes.

nssm code package

The functions to reconstruct the sound sheet data are packaged in the +nssm namespace. There are three inner namespaces:

• +recon contains all functions required to reconstruct sound sheet RFData to images.
• +sequence contains some helper functions for real time beamforming in the NSSM Verasonics imaging sequence.
• +utils contains some utility functions (e.g. for rearranging RFData).

All functions are documented and help can be viewed using e.g.:

help nssm.recon.reconDAS

License

This project is licensed under the CC BY-SA 4.0 License. See the LICENSE file for details.