Nonlinear sound-sheet microscopy: imaging opaque organs at the capillary and cellular scale

This dataset accompanies the article entitled: "Nonlinear sound-sheet microscopy: imaging opaque organs at the capillary and cellular scale".

Wells with E. Coli (Wells_EColi.zip)

Codes are hosted here

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. The file demo_navigate_3D_NSSM_data.m can be used to view the volumes.

mARG expression in orthopic tumors (mArg_tumors.zip)

Codes are hosted here

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. The file demo_navigate_3D_NSSM_data.m can be used to view the volumes.

Nonlinear Soundsheet Localization Microscopy (NSSLM_zenodo_archive.zip)

Codes are hosted here

A zip compressed dataset containing beamformed images and post-processed trajectories for Nonlinear Soundsheet Localization Microscopy.

The files ImgNSSM_00x.mat are 4D data arrays of size (157x160x2x2100). They hold 2 soundsheets repeated for 2100 frames at 1000Hz (more details are provided in the Material and Methods section of accompanying papers). Use this dataset to run script processNSSLM.m

The file Params.mat is a file containing the ULM structure. This comprises the fields necessary to execute ULM codes from the PALA toolbox

A folder named Trajectories. This contains 50 files. Each contains the trajectories obtained from NSSLM processing of the entire sequence for soundsheet indexed 1 in the 4D matrix. Use this dataset to run script renderingNSSLM.m

Each of these datasets is to be used in conjunction with the different example scripts given on here.

Codes hosted on github

For accompanying codes, please refer to:

https://github.com/MarescaRenaudLabs/NSSM/releases/tag/v1.0.0

https://github.com/MarescaRenaudLabs/NSSLM/releases/tag/v1.0.0