from pheno_utils import PhenoLoader004-liver_ultrasound
Liver ultrasound dataset
Liver ultrasound was performed using the Supersonic Aixplorer MACH 30 (Hologic, USA). The Supersonic Imagine Aixplorer is an ultrasound device that is able to measure the liver’s stiffness, viscosity, attenuation and sound speed to diagnose and monitor liver conditions such as steatosis, fibrosis and inflammation. The device uses several ultrasound-based measures, including Speed of Sound (SSp.PLUS), Attenuation Index (Att.PLUS), Viscosity (Vi.PLUS) and Elasticity (Two-Dimensional ShareWave Elastography (2D-SWE)) to evaluate the liver and improve diagnosis performance. These measurements have been shown to be correlated to different stages of liver conditions.
Ultrasound-based liver measurements were performed using ShearWave Elastography (2D- SWE.PLUS) for elasticity assessment, sound speed Plane-wave ultrasound and attenuation. Plane-wave ultrasound was measured for assessment of liver steatosis (fatness) and viscosity plane-wave ultrasound for assessment of viscosity as a marker of inflammation. Measurements were performed with a C6-1X convex transducer using the UltraFast software available on the Mach 30 ultrasound system. US images of the liver were also saved.
Measurement protocol: All patients were examined in supine position, with the right arm elevated above the head, by an intercostal approach, in the right liver lobe. Acquisitions were performed during neutral respiratory apnea. Initially the Attenuation and Speed of Sound were measured from a homogeneous area of the liver parenchyma free of vessels or other structures. Measurements were performed from 3 different liver regions. 2D-SWE and viscosity were then measured from 3 different locations in an area of relative uniform elasticity, at a depth of 3–5 cm using stability index tool (SI) derived from the spatial and temporal stiffness stability at a stability index >90%.
Data availability:
The information is stored in 2 parquet files: liver_ultrasound.parquetand liver_ultrasound_aggregated.parquet
pl = PhenoLoader('liver_ultrasound')
plPhenoLoader for liver_ultrasound with
58 fields
3 tables: ['liver_ultrasound', 'liver_ultrasound_aggregated', 'age_sex']Data dictionary
pl.dict| field_string | description_string | folder_id | feature_set | field_type | strata | data_coding | array | pandas_dtype | bulk_file_extension | relative_location | units | bulk_dictionary | sampling_rate | transformation | list_of_tags | stability | sexed | debut | completed | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| tabular_field_name | ||||||||||||||||||||
| timezone | Timezone | Timezone | 4 | liver_ultrasound | Categorical (single) | Collection time | 001_03 | Multiple | category | NaN | liver_ultrasound/liver_ultrasound.parquet | NaN | NaN | NaN | NaN | NaN | Accruing | Both sexes | 2021-08-16 | NaN |
| collection_date | Collection date (YYYY-MM-DD) | Collection date (YYYY-MM-DD) | 4 | liver_ultrasound | Date | Collection time | NaN | Multiple | datetime64[ns] | NaN | liver_ultrasound/liver_ultrasound.parquet | NaN | NaN | NaN | NaN | NaN | Accruing | Both sexes | 2021-08-16 | NaN |
| collection_timestamp | Collection timestamp | Collection timestamp | 4 | liver_ultrasound | Datetime | Collection time | NaN | Multiple | datetime64[ns, Asia/Jerusalem] | NaN | liver_ultrasound/liver_ultrasound.parquet | NaN | NaN | NaN | NaN | NaN | Accruing | Both sexes | 2021-08-16 | NaN |
| liver_ultrasound_qbox_depth | Liver ultrasound qbox depth | Liver ultrasound ShearWave Elastography (SWE) ... | 4 | liver_ultrasound | Continuous | Auxiliary | NaN | Multiple | float | NaN | liver_ultrasound/liver_ultrasound.parquet | cm | NaN | NaN | NaN | NaN | Accruing | Both sexes | 2021-08-16 | NaN |
| liver_ultrasound_qbox_diameter | Liver ultrasound qbox diameter | Liver ultrasound SWE Q-Box diameter | 4 | liver_ultrasound | Continuous | Auxiliary | NaN | Multiple | float | NaN | liver_ultrasound/liver_ultrasound.parquet | mm | NaN | NaN | NaN | NaN | Accruing | Both sexes | 2021-08-16 | NaN |
| liver_ultrasound_stability_index | Liver ultrasound stability index | Liver ultrasound stability index tool (SI) for... | 4 | liver_ultrasound | Continuous | Auxiliary | NaN | Multiple | float | NaN | liver_ultrasound/liver_ultrasound.parquet | NaN | NaN | NaN | NaN | NaN | Accruing | Both sexes | 2021-08-16 | NaN |
| elasticity_qbox_minimum | Elasticity (qbox minimum) | Elasticity, minimum value measured within the ... | 4 | liver_ultrasound | Continuous | Primary | NaN | Multiple | float | NaN | liver_ultrasound/liver_ultrasound.parquet | kPa | NaN | NaN | NaN | NaN | Accruing | Both sexes | 2021-08-16 | NaN |
| elasticity_qbox_maximum | Elasticity (qbox maximum) | Elasticity, maximum value measured within the ... | 4 | liver_ultrasound | Continuous | Primary | NaN | Multiple | float | NaN | liver_ultrasound/liver_ultrasound.parquet | kPa | NaN | NaN | NaN | NaN | Accruing | Both sexes | 2021-08-16 | NaN |
| elasticity_qbox_median | Elasticity (qbox median) | Elasticity, median of the values measured with... | 4 | liver_ultrasound | Continuous | Primary | NaN | Multiple | float | NaN | liver_ultrasound/liver_ultrasound.parquet | kPa | NaN | NaN | NaN | NaN | Accruing | Both sexes | 2021-08-16 | NaN |
| elasticity_qbox_standard_deviation | Elasticity (qbox standard deviation) | Elasticity, standard deviation of values measu... | 4 | liver_ultrasound | Continuous | Primary | NaN | Multiple | float | NaN | liver_ultrasound/liver_ultrasound.parquet | kPa | NaN | NaN | NaN | NaN | Accruing | Both sexes | 2021-08-16 | NaN |
| elasticity_qbox_mean | Elasticity (qbox mean) | Elasticity, mean of the values measured within... | 4 | liver_ultrasound | Continuous | Primary | NaN | Multiple | float | NaN | liver_ultrasound/liver_ultrasound.parquet | kPa | NaN | NaN | NaN | NaN | Accruing | Both sexes | 2021-08-16 | NaN |
| velocity_qbox_minimum | Velocity (qbox minimum) | Velocity of the shear wave, minimum value meas... | 4 | liver_ultrasound | Continuous | Primary | NaN | Multiple | float | NaN | liver_ultrasound/liver_ultrasound.parquet | m/s | NaN | NaN | NaN | NaN | Accruing | Both sexes | 2021-08-16 | NaN |
| velocity_qbox_maximum | Velocity (qbox maximum) | Velocity of the shear wave, maximum value meas... | 4 | liver_ultrasound | Continuous | Primary | NaN | Multiple | float | NaN | liver_ultrasound/liver_ultrasound.parquet | m/s | NaN | NaN | NaN | NaN | Accruing | Both sexes | 2021-08-16 | NaN |
| velocity_qbox_median | Velocity (qbox median) | Velocity of the shear wave, median of the valu... | 4 | liver_ultrasound | Continuous | Primary | NaN | Multiple | float | NaN | liver_ultrasound/liver_ultrasound.parquet | m/s | NaN | NaN | NaN | NaN | Accruing | Both sexes | 2021-08-16 | NaN |
| velocity_qbox_standard_deviation | Velocity (qbox standard deviation) | Velocity of the shear wave, standard deviation... | 4 | liver_ultrasound | Continuous | Primary | NaN | Multiple | float | NaN | liver_ultrasound/liver_ultrasound.parquet | m/s | NaN | NaN | NaN | NaN | Accruing | Both sexes | 2021-08-16 | NaN |
| velocity_qbox_mean | Velocity (qbox mean) | Velocity of the shear wave, mean of the values... | 4 | liver_ultrasound | Continuous | Primary | NaN | Multiple | float | NaN | liver_ultrasound/liver_ultrasound.parquet | m/s | NaN | NaN | NaN | NaN | Accruing | Both sexes | 2021-08-16 | NaN |
| viscosity_qbox_median | Viscosity (qbox median) | Viscosity, median of the values measured withi... | 4 | liver_ultrasound | Continuous | Primary | NaN | Multiple | float | NaN | liver_ultrasound/liver_ultrasound.parquet | Pa.s | NaN | NaN | NaN | NaN | Accruing | Both sexes | 2021-08-16 | NaN |
| viscosity_qbox_standard_deviation | Viscosity (qbox standard deviation) | Viscosity, standard deviation of values measur... | 4 | liver_ultrasound | Continuous | Primary | NaN | Multiple | float | NaN | liver_ultrasound/liver_ultrasound.parquet | Pa.s | NaN | NaN | NaN | NaN | Accruing | Both sexes | 2021-08-16 | NaN |
| viscosity_qbox_mean | Viscosity (qbox mean) | Viscosity, mean of the values measured within ... | 4 | liver_ultrasound | Continuous | Primary | NaN | Multiple | float | NaN | liver_ultrasound/liver_ultrasound.parquet | Pa.s | NaN | NaN | NaN | NaN | Accruing | Both sexes | 2021-08-16 | NaN |
| dispersion_qbox_median | Dispersion (qbox median) | Shear wave dispersion median of the values mea... | 4 | liver_ultrasound | Continuous | Primary | NaN | Multiple | float | NaN | liver_ultrasound/liver_ultrasound.parquet | (m/s)/kHz | NaN | NaN | NaN | NaN | Accruing | Both sexes | 2021-08-16 | NaN |
| dispersion_qbox_standard_deviation | Dispersion (qbox standard deviation) | Shear wave dispersion standard deviation of th... | 4 | liver_ultrasound | Continuous | Primary | NaN | Multiple | float | NaN | liver_ultrasound/liver_ultrasound.parquet | (m/s)/kHz | NaN | NaN | NaN | NaN | Accruing | Both sexes | 2021-08-16 | NaN |
| dispersion_qbox_mean | Dispersion (qbox mean) | Shear wave dispersion mean of the values measu... | 4 | liver_ultrasound | Continuous | Primary | NaN | Multiple | float | NaN | liver_ultrasound/liver_ultrasound.parquet | (m/s)/kHz | NaN | NaN | NaN | NaN | Accruing | Both sexes | 2021-08-16 | NaN |
| attenuation_coefficient_qbox | Attenuation coefficient (qbox) | Attenuation Plane-Wave Ultrasound (Att.P) coef... | 4 | liver_ultrasound | Continuous | Primary | NaN | Multiple | float | NaN | liver_ultrasound/liver_ultrasound.parquet | dB/cm/MHz | NaN | NaN | NaN | NaN | Accruing | Both sexes | 2021-08-16 | NaN |
| speed_of_sound_qbox | Speed of sound (qbox) | Sound Speed Plane-Wave Ultrasound (SSp.PLUS) | 4 | liver_ultrasound | Continuous | Primary | NaN | Multiple | float | NaN | liver_ultrasound/liver_ultrasound.parquet | m/s | NaN | NaN | NaN | NaN | Accruing | Both sexes | 2021-08-16 | NaN |
| elasticity_mean_minimum_of_qboxes | Elasticity (mean minimum of qboxes) | Elasticity (mean minimum of qboxes) | 4 | liver_ultrasound_aggregated | Continuous | Primary | NaN | Multiple | float | NaN | liver_ultrasound/liver_ultrasound_aggregated.p... | kPa | NaN | NaN | NaN | NaN | Accruing | Both sexes | 2021-08-16 | NaN |
| elasticity_mean_maximum_of_qboxes | Elasticity (mean maximum of qboxes) | Elasticity (mean maximum of qboxes) | 4 | liver_ultrasound_aggregated | Continuous | Primary | NaN | Multiple | float | NaN | liver_ultrasound/liver_ultrasound_aggregated.p... | kPa | NaN | NaN | NaN | NaN | Accruing | Both sexes | 2021-08-16 | NaN |
| elasticity_mean_median_of_qboxes | Elasticity (mean median of qboxes) | Elasticity (mean median of qboxes) | 4 | liver_ultrasound_aggregated | Continuous | Primary | NaN | Multiple | float | NaN | liver_ultrasound/liver_ultrasound_aggregated.p... | kPa | NaN | NaN | NaN | NaN | Accruing | Both sexes | 2021-08-16 | NaN |
| elasticity_mean_standard_deviation_of_qboxes | Elasticity (mean standard deviation of qboxes) | Elasticity (mean standard deviation of qboxes) | 4 | liver_ultrasound_aggregated | Continuous | Primary | NaN | Multiple | float | NaN | liver_ultrasound/liver_ultrasound_aggregated.p... | kPa | NaN | NaN | NaN | NaN | Accruing | Both sexes | 2021-08-16 | NaN |
| elasticity_mean_mean_of_qboxes | Elasticity (mean mean of qboxes) | Elasticity (mean mean of qboxes) | 4 | liver_ultrasound_aggregated | Continuous | Primary | NaN | Multiple | float | NaN | liver_ultrasound/liver_ultrasound_aggregated.p... | kPa | NaN | NaN | NaN | NaN | Accruing | Both sexes | 2021-08-16 | NaN |
| elasticity_median_minimum_of_qboxes | Elasticity (median minimum of qboxes) | Elasticity (median minimum of qboxes) | 4 | liver_ultrasound_aggregated | Continuous | Primary | NaN | Multiple | float | NaN | liver_ultrasound/liver_ultrasound_aggregated.p... | kPa | NaN | NaN | NaN | NaN | Accruing | Both sexes | 2021-08-16 | NaN |
| elasticity_median_maximum_of_qboxes | Elasticity (median maximum of qboxes) | Elasticity (median maximum of qboxes) | 4 | liver_ultrasound_aggregated | Continuous | Primary | NaN | Multiple | float | NaN | liver_ultrasound/liver_ultrasound_aggregated.p... | kPa | NaN | NaN | NaN | NaN | Accruing | Both sexes | 2021-08-16 | NaN |
| elasticity_median_median_of_qboxes | Elasticity (median median of qboxes) | Elasticity (median median of qboxes) | 4 | liver_ultrasound_aggregated | Continuous | Primary | NaN | Multiple | float | NaN | liver_ultrasound/liver_ultrasound_aggregated.p... | kPa | NaN | NaN | NaN | NaN | Accruing | Both sexes | 2021-08-16 | NaN |
| elasticity_median_standard_deviation_of_qboxes | Elasticity (median standard deviation of qboxes) | Elasticity (median standard deviation of qboxes) | 4 | liver_ultrasound_aggregated | Continuous | Primary | NaN | Multiple | float | NaN | liver_ultrasound/liver_ultrasound_aggregated.p... | kPa | NaN | NaN | NaN | NaN | Accruing | Both sexes | 2021-08-16 | NaN |
| elasticity_median_mean_of_qboxes | Elasticity (median mean of qboxes) | Elasticity (median mean of qboxes) | 4 | liver_ultrasound_aggregated | Continuous | Primary | NaN | Multiple | float | NaN | liver_ultrasound/liver_ultrasound_aggregated.p... | kPa | NaN | NaN | NaN | NaN | Accruing | Both sexes | 2021-08-16 | NaN |
| velocity_mean_minimum_of_qboxes | Velocity (mean minimum of qboxes) | Velocity (mean minimum of qboxes) | 4 | liver_ultrasound_aggregated | Continuous | Primary | NaN | Multiple | float | NaN | liver_ultrasound/liver_ultrasound.parquet | m/s | NaN | NaN | NaN | NaN | Accruing | Both sexes | 2021-08-16 | NaN |
| velocity_mean_maximum_of_qboxes | Velocity (mean maximum of qboxes) | Velocity (mean maximum of qboxes) | 4 | liver_ultrasound_aggregated | Continuous | Primary | NaN | Multiple | float | NaN | liver_ultrasound/liver_ultrasound.parquet | m/s | NaN | NaN | NaN | NaN | Accruing | Both sexes | 2021-08-16 | NaN |
| velocity_mean_median_of_qboxes | Velocity (mean median of qboxes) | Velocity (mean median of qboxes) | 4 | liver_ultrasound_aggregated | Continuous | Primary | NaN | Multiple | float | NaN | liver_ultrasound/liver_ultrasound.parquet | m/s | NaN | NaN | NaN | NaN | Accruing | Both sexes | 2021-08-16 | NaN |
| velocity_mean_standard_deviation_of_qboxes | Velocity (mean standard deviation of qboxes) | Velocity (mean standard deviation of qboxes) | 4 | liver_ultrasound_aggregated | Continuous | Primary | NaN | Multiple | float | NaN | liver_ultrasound/liver_ultrasound.parquet | m/s | NaN | NaN | NaN | NaN | Accruing | Both sexes | 2021-08-16 | NaN |
| velocity_mean_mean_of_qboxes | Velocity (mean mean of qboxes) | Velocity (mean mean of qboxes) | 4 | liver_ultrasound_aggregated | Continuous | Primary | NaN | Multiple | float | NaN | liver_ultrasound/liver_ultrasound.parquet | m/s | NaN | NaN | NaN | NaN | Accruing | Both sexes | 2021-08-16 | NaN |
| velocity_median_minimum_of_qboxes | Velocity (median minimum of qboxes) | Velocity (median minimum of qboxes) | 4 | liver_ultrasound_aggregated | Continuous | Primary | NaN | Multiple | float | NaN | liver_ultrasound/liver_ultrasound.parquet | m/s | NaN | NaN | NaN | NaN | Accruing | Both sexes | 2021-08-16 | NaN |
| velocity_median_maximum_of_qboxes | Velocity (median maximum of qboxes) | Velocity (median maximum of qboxes) | 4 | liver_ultrasound_aggregated | Continuous | Primary | NaN | Multiple | float | NaN | liver_ultrasound/liver_ultrasound.parquet | m/s | NaN | NaN | NaN | NaN | Accruing | Both sexes | 2021-08-16 | NaN |
| velocity_median_median_of_qboxes | Velocity (median median of qboxes) | Velocity (median median of qboxes) | 4 | liver_ultrasound_aggregated | Continuous | Primary | NaN | Multiple | float | NaN | liver_ultrasound/liver_ultrasound.parquet | m/s | NaN | NaN | NaN | NaN | Accruing | Both sexes | 2021-08-16 | NaN |
| velocity_median_standard_deviation_of_qboxes | Velocity (median standard deviation of qboxes) | Velocity (median standard deviation of qboxes) | 4 | liver_ultrasound_aggregated | Continuous | Primary | NaN | Multiple | float | NaN | liver_ultrasound/liver_ultrasound.parquet | m/s | NaN | NaN | NaN | NaN | Accruing | Both sexes | 2021-08-16 | NaN |
| velocity_median_mean_of_qboxes | Velocity (median mean of qboxes) | Velocity (median mean of qboxes) | 4 | liver_ultrasound_aggregated | Continuous | Primary | NaN | Multiple | float | NaN | liver_ultrasound/liver_ultrasound.parquet | m/s | NaN | NaN | NaN | NaN | Accruing | Both sexes | 2021-08-16 | NaN |
| viscosity_mean_median_of_qboxes | Viscosity (mean median of qboxes) | Viscosity (mean median of qboxes) | 4 | liver_ultrasound_aggregated | Continuous | Primary | NaN | Multiple | float | NaN | liver_ultrasound/liver_ultrasound.parquet | Pa.s | NaN | NaN | NaN | NaN | Accruing | Both sexes | 2021-08-16 | NaN |
| viscosity_mean_standard_deviation_of_qboxes | Viscosity (mean standard deviation of qboxes) | Viscosity (mean standard deviation of qboxes) | 4 | liver_ultrasound_aggregated | Continuous | Primary | NaN | Multiple | float | NaN | liver_ultrasound/liver_ultrasound.parquet | Pa.s | NaN | NaN | NaN | NaN | Accruing | Both sexes | 2021-08-16 | NaN |
| viscosity_mean_mean_of_qboxes | Viscosity (mean mean of qboxes) | Viscosity (mean mean of qboxes) | 4 | liver_ultrasound_aggregated | Continuous | Primary | NaN | Multiple | float | NaN | liver_ultrasound/liver_ultrasound.parquet | Pa.s | NaN | NaN | NaN | NaN | Accruing | Both sexes | 2021-08-16 | NaN |
| viscosity_median_median_of_qboxes | Viscosity (median median of qboxes) | Viscosity (median median of qboxes) | 4 | liver_ultrasound_aggregated | Continuous | Primary | NaN | Multiple | float | NaN | liver_ultrasound/liver_ultrasound.parquet | Pa.s | NaN | NaN | NaN | NaN | Accruing | Both sexes | 2021-08-16 | NaN |
| viscosity_median_standard_deviation_of_qboxes | Viscosity (median standard deviation of qboxes) | Viscosity (median standard deviation of qboxes) | 4 | liver_ultrasound_aggregated | Continuous | Primary | NaN | Multiple | float | NaN | liver_ultrasound/liver_ultrasound.parquet | Pa.s | NaN | NaN | NaN | NaN | Accruing | Both sexes | 2021-08-16 | NaN |
| viscosity_median_mean_of_median | Viscosity (median mean of median) | Viscosity (median mean of median) | 4 | liver_ultrasound_aggregated | Continuous | Primary | NaN | Multiple | float | NaN | liver_ultrasound/liver_ultrasound.parquet | Pa.s | NaN | NaN | NaN | NaN | Accruing | Both sexes | 2021-08-16 | NaN |
| dispersion_mean_median_of_qboxes | Dispersion (mean median of qboxes) | Dispersion (mean median of qboxes) | 4 | liver_ultrasound_aggregated | Continuous | Primary | NaN | Multiple | float | NaN | liver_ultrasound/liver_ultrasound.parquet | (m/s)/kHz | NaN | NaN | NaN | NaN | Accruing | Both sexes | 2021-08-16 | NaN |
| dispersion_mean_standard_deviation_of_qboxes | Dispersion (mean standard deviation of qboxes) | Dispersion (mean standard deviation of qboxes) | 4 | liver_ultrasound_aggregated | Continuous | Primary | NaN | Multiple | float | NaN | liver_ultrasound/liver_ultrasound.parquet | (m/s)/kHz | NaN | NaN | NaN | NaN | Accruing | Both sexes | 2021-08-16 | NaN |
| dispersion_mean_mean_of_qboxes | Dispersion (mean mean of qboxes) | Dispersion (mean mean of qboxes) | 4 | liver_ultrasound_aggregated | Continuous | Primary | NaN | Multiple | float | NaN | liver_ultrasound/liver_ultrasound.parquet | (m/s)/kHz | NaN | NaN | NaN | NaN | Accruing | Both sexes | 2021-08-16 | NaN |
| dispersion_median_median_of_qboxes | Dispersion (median median of qboxes) | Dispersion (median median of qboxes) | 4 | liver_ultrasound_aggregated | Continuous | Primary | NaN | Multiple | float | NaN | liver_ultrasound/liver_ultrasound.parquet | (m/s)/kHz | NaN | NaN | NaN | NaN | Accruing | Both sexes | 2021-08-16 | NaN |
| dispersion_median_standard_deviation_of_qboxes | Dispersion (median standard deviation of qboxes) | Dispersion (median standard deviation of qboxes) | 4 | liver_ultrasound_aggregated | Continuous | Primary | NaN | Multiple | float | NaN | liver_ultrasound/liver_ultrasound.parquet | (m/s)/kHz | NaN | NaN | NaN | NaN | Accruing | Both sexes | 2021-08-16 | NaN |
| dispersion_median_mean_of_median | Dispersion (median mean of median) | Dispersion (median mean of median) | 4 | liver_ultrasound_aggregated | Continuous | Primary | NaN | Multiple | float | NaN | liver_ultrasound/liver_ultrasound.parquet | (m/s)/kHz | NaN | NaN | NaN | NaN | Accruing | Both sexes | 2021-08-16 | NaN |
Plot histogram and ecdf for elasticity_median_median_of_qboxes at baseline visit
from pheno_utils.basic_plots import hist_ecdf_plots
col = "elasticity_median_median_of_qboxes"
df = pl[[col] + ["age", "sex", "collection_date"]].loc[:,:,"00_00_visit",0,:]
# plot histogram and ecdf
hist_ecdf_plots(df.dropna(subset=[col,"sex", "age"]), col, gender_col="sex")
# stats
display(df[col].describe().to_frame().T)
| count | mean | std | min | 25% | 50% | 75% | max | |
|---|---|---|---|---|---|---|---|---|
| elasticity_median_median_of_qboxes | 6757.0 | 5.017764 | 1.190037 | 2.65 | 4.24 | 4.84 | 5.56 | 29.6 |