This "readme - Stähli et al 2021 Trans Med Imag.txt" file was generated on 2024-04-02 by 
Michael Jaeger, Institute of Applied Physics, University of Bern 

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GENERAL INFORMATION
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1. Title of dataset: "Raw data used in Stähli et al. 2021 Trans Med Imag 40(2)" 

2. Short description: 
Echo ultrasound raw data used in "the paper": 
"Bayesian approach for a robust speed-of-sound reconstruction using pulse-echo ultrasound" 
Stähli et al. 2021, IEEE Trans Med Imag 40(2) 457-467, doi: 10.1109/TMI.2020.3029286 

3. Contributor information: 
Patrick Stähli, first author and data creator: code development, phantom building, data acquisition, data analysis, manuscript writing. 
Martin Frenz, principal investigator: manuscript editing 
Michael Jaeger, group leader: scientific supervision, manuscript editing, data curation 
 
For questions, contact: 
Michael Jaeger, group leader 
Institute of Applied Physics, University of Bern, Sidlerstrasse 5, 3012 Bern, Switzerland 
michael.jaeger@unibe.ch 

4. Date of data collection: 
2019-01-15 to 2019-07-19 

5. Geographic location of data collection:  
Bern, Switzerland 

6. Keywords:  
Ultrasound tomography, reflection mode, multimodal imaging, inverse problem

7. Information about funding sources that supported the collection of the data:  
Funding agency: Swiss National Science Foundation 
Grant number: 205320_178038 
Funding agency: European Union’s Horizon 2020 research and innovation
programme 
Grant number: 732411 
Funding agency: Photonics Private Public Partnership 
Funding agency: Swiss State Secretariat for Education,
Research and Innovation (SERI) 
Grant number: 
16.0162 

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SHARING/ACCESS INFORMATION 
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1. Licenses/restrictions placed on the data: 
Attribution NonCommercial-NoDerivs CC BY-NC-SA

2. Links to publications that cite or use the data: 
DOI 10.1109/TMI.2020.3029286 
https://ieeexplore.ieee.org/document/9216009 

3. Was data derived from another source? No 

4. Recommended citation for this dataset: 
Patrick Stähli, Martin Frenz, Michael Jaeger "Raw data used in Stähli et al. 2021 Trans Med Imag 40(2)" 2024, BORIS, https://doi.org/10.48620/386

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DATA & FILE OVERVIEW  
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1. File list: 
The files are named according to the nomenclatura in the figures in the paper. In addition, there are 4 files containing data for system calibration. Calibration was used for the results shown in the figures, even though it was not mentionned in the paper. The calibration procedure is, however, described in Jaeger et al. "Pulse-echo speed-of-sound imaging using convex probes" 2022 Phys Med Biol 67, 215016-1--17, doi: 10.1088/1361-6560/ac96c6

Fig. 9: 
phantom_P1.pw.mat
phantom_P2.pw.mat
phantom_P3.pw.mat 

Fig. 10: 
invivo_A_1.pw.mat 
invivo_A_2.pw.mat 
invivo_A_3.pw.mat 
invivo_B_1.pw.mat 
invivo_B_2.pw.mat 
invivo_B_3.pw.mat 
invivo_C_1.pw.mat 
invivo_C_2.pw.mat 
invivo_C_3.pw.mat 
invivo_D_1.pw.mat 
invivo_D_2.pw.mat 
invivo_D_3.pw.mat 

Calibration: 
calibration_1.pw.mat 
calibration_2.pw.mat
calibration_3.pw.mat
calibration_4.pw.mat

2. Relationship between files: 
none 

3. Are there multiple versions of the dataset? no 

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METHODOLOGICAL INFORMATION  
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1. Description of methods used for collection/generation of data: 
The data were acquired using a L7-4 linear vascular probe (ATL Philips, WA, USA), 
connected to a Vantage 64 LE (Verasonics Inc., WA, USA) research ultrasound system. 

for details see: 
"Bayesian approach for a robust speed-of-sound reconstruction using pulse-echo ultrasound" 
Stähli et al. 2021, IEEE Trans Med Imag 40(2) 457-467, doi: 10.1109/TMI.2020.3029286 

2. Methods for processing the data 
For ease of use, the raw data from the Verasonics system was converted to a self-explaining format. 
Each .mat file contains two variables: 
"metadata" a structure with fields describing important parameters for the interpreation of the data 
"rawdata" a matrix containing the signal values, where dimensions correspond to (time, element index, acquisition angle) 

3. Instrument- or software-specific information needed to interpret the data: 
Information needed for interpretation are found in the "metadata" variable 

4. Standards and calibration information: 
No standards or calibration were used for producing the data. When processing the data, however, note that calibration data is available (see above) for calibrating the desired results. 

5. Quality-assurance procedures: 
None 

6. People involved with sample collection, processing, analysis, curation: 
Patrick Stähli, Michael Jaeger 

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DATA-SPECIFIC INFORMATION  
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"phantom_P...pw.mat" were acquired from phantoms made of gelatine, cellulose, oil in gelatine. For further detail read the paper. The reference SoS values were: 
for layer C1: 1490 m/s
for layer C2: 1585 m/s
for layer C3: 1490 m/s
for layer C4 A-C: 1525 m/s, 1555 m/s, 1585 m/s 

"invivo_P...pw.mat" were acquired from a healthy volunteer in different locations as described in the paper. 

"calibration ...pw.mat" were acquired from a phantom made of agar and cellulose, in slightly different positions with decorrelated speckle. The reference SoS value is 1490 m/s