chaohuang-ch/akebia

Scripts, functions and open platform (Akebia) for sensing Ultrasound Localization Microscopy (sULM)

Version 1.0, 15.01.2023

Repository to share scripts and functions for "Sensing Ultrasound Localization Microscopy for the visualization of glomeruli in living rats and humans" article, and Akebia software. All functions are usable with agreement from their owner.

Authors : Louise Denis, Jacques Battaglia. CNRS, Sorbonne Université, INSERM

Directed by: Olivier Couture, Research Director CNRS, Sorbonne Université, INSERM.

Laboratoire d'Imagerie Biomédicale, Team PPM. 15 rue de l'Ecole de Médecine, 75006, Paris, France.

Code Available under Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International

Partly funded by the European Research Council under the European Union Horizon H2020 programme / ERC Consolidator grant agreement No 772786-ResolveStroke

Corresponding authors

• Article : Louise Denis, Sylvain Bodard

• Scripts, and codes : Louise Denis, Jacques Battaglia

• Materials, collaborations, rights and others: Olivier Couture

Academic references to be cited

Details of the code in the article by Denis, Bodard, Hingot, Chavignon, Battaglia, Renault, Lager, Aissani, Hélénon, Correas, and Couture. Sensing Ultrasound Localization Microscopy for the visualization of glomeruli in living rats and humans, eBioMedicine, 2023.

Inspired from PALA / Lotus: Heiles, Chavignon et al., Performance benchmarking of microbubble-localization algorithms for ultrasound localization microscopy, Nature Biomedical Engineering, 2022 (10.1038/s41551-021-00824-8)

General description of super-resolution in: Couture et al., Ultrasound localization microscopy and super-resolution: A state of the art, IEEE UFFC 2018.

Related Dataset

In-vivo rat 14 beamformed dataset is available in Zenodo (10.5281/zenodo.6811910).

Raw dataset (RF) can also be found in another Zenodo repository (10.5281/zenodo.6811910).

Patients imaging data are not available due to ethical, medical and legislative considerations towards personal information.

Folder's organization

• /Example script

  This folder contains an example script of sULM and all functions called in the Akebia software. The script generates 3 composite images, i.e. slow and rapid tracking are superimposed:

  • Image density based on microbubbles counts: pixel intensity codes the number of microbubbles crossing this pixel

  • Image density with axial color encoding: pixel intensity codes the number of microbubbles crossing upward/downward

  • Velocity magnitude image: pixel intensity represents the average bubble velocity in mm/s

  More details in the README inside this folder.

• /Software_Akebia

  This folder contains the open platform Akebia. It is a standalone application and there's no need to own Matlab to install this software. More details in the README and the User Guide inside this folder.

• /Results

  Example of images generated by the example script Akebia_example_script.m or by the Akebia software after processing the In-vivo rat 14 dataset : blocks 10 to 20 and 27 to 32 of 800 frames each.

  Density.tif, Directivity.tif and Velocity.tif are presented here. But you can also find HumanDensity.tif, HumanDirectivity.tif and HumanVelocity.tif of patient number 1 (same as in the article). More details in the README inside /Example script and /Software Akebia.

Disclaimer

THIS SOFTWARE IS PROVIDED BY THE AUTHORS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE AUTHORS AND CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

by LD, JB, OC.