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

<p>This dataset accompanies the article entitled: "Nonlinear sound-sheet microscopy: imaging opaque organs at the capillary and cellular scale".</p> <div> <h3><strong>Wells with E. Coli (Wells_EColi.zip)</strong></h3> <p><strong>Codes are hosted <a title="NSSM github repo" href="https://github.com/MarescaRenaudLabs/NSSM/releases/tag/v1.0.0" target="_blank" rel="noopener">here</a></strong></p> </div> <p>Representative dataset for paper figure 2D,E. The file&nbsp;<code>RFData_planes_figure_2E.mat</code>&nbsp;contains the RFData and the required parameters to reconstruct two orthogonal sound sheets, in SSM and NSSM mode. The file&nbsp;<code>demo_reconstruct_orthogonal_NSSM_images.m</code>&nbsp;shows how to reconstruct the sound sheet data.</p> <p>The file&nbsp;<code>beamformed_volume_figure_2E.mat</code>&nbsp;contains beamformed SSM and NSSM volumes as displayed in figure 2G. The file&nbsp;<code>demo_navigate_3D_NSSM_data.m</code>&nbsp;can be used to view the volumes.</p> <div> <h3><strong>mARG expression in orthopic tumors (mArg_tumors.zip)</strong></h3> <p><strong>Codes are hosted <a title="NSSM github repo" href="https://github.com/MarescaRenaudLabs/NSSM/releases/tag/v1.0.0" target="_blank" rel="noopener">here</a></strong></p> </div> <p>Representative dataset for paper figure 3B. The file&nbsp;<code>RFData_planes_figure_3B.mat</code>&nbsp;contains the RFData and the required parameters to reconstruct two orthogonal sound sheets, in SSM and NSSM mode. The file&nbsp;<code>demo_reconstruct_orthogonal_NSSM_images.m</code>&nbsp;shows how to reconstruct the sound sheet data.</p> <p>The file&nbsp;<code>beamformed_volume_figure_3B.mat</code>&nbsp;contains beamformed SSM and NSSM volumes as displayed in figure 3C. The file&nbsp;<code>demo_navigate_3D_NSSM_data.m</code> can be used to view the volumes.</p> <h3><strong>Nonlinear Soundsheet Localization Microscopy (NSSLM_zenodo_archive.zip)</strong></h3> <p><strong>Codes are hosted <a title="NSSLM github repo" href="https://github.com/MarescaRenaudLabs/NSSLM/releases/tag/v1.0.0" target="_blank" rel="noopener">here</a></strong></p> <p>A zip compressed dataset containing beamformed images and post-processed trajectories for Nonlinear Soundsheet Localization Microscopy.</p> <ul> <li>The files <code>ImgNSSM_00x.mat</code> 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 <code>processNSSLM.m</code></li> <li>The file <code>Params.mat</code> is a file containing the&nbsp;<code>ULM</code> structure. This comprises the fields necessary to execute ULM codes from the <a href="https://github.com/AChavignon/PALA" target="_blank" rel="noopener">PALA toolbox</a></li> <li>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.&nbsp;Use this dataset to run script <code>renderingNSSLM.m</code></li> </ul> <p>Each of these datasets is to be used in conjunction with the different example scripts given on <strong><a title="NSSLM github repo" href="https://github.com/MarescaRenaudLabs/NSSLM/releases/tag/v1.0.0" target="_blank" rel="noopener">here</a></strong>.</p> <h3>Codes hosted on github</h3> <p>For accompanying codes, please refer to:</p> <ul> <li>https://github.com/MarescaRenaudLabs/NSSM/releases/tag/v1.0.0</li> <li>https://github.com/MarescaRenaudLabs/NSSLM/releases/tag/v1.0.0</li> </ul>