from pheno_utils import PhenoLoader003-fundus
Fundus images dataset
Fundus imaging allows for the visualization of the interior surface of the eye, known as the fundus; and used to examine structures such as the optic disc, retina, and retinal microvasculature. This procedure is commonly used to diagnose and monitor a variety of eye diseases.
Fundus imaging is a type of medical imaging technique that is used to obtain detailed, high-resolution images of the back of the eye, including the retina, the optic nerve, and the macula, an oval-shaped area in the center of the retina used for central vision. These images can provide important information about the health of the eye and can be used to diagnose and monitor a variety of eye diseases and conditions.
One of the key features that can be seen in fundus images is the retinal microvasculature, which refers to the network of small blood vessels that supply blood to the retina. The appearance and structure of the retinal microvasculature can provide information about the health of the eye and can be used to diagnose and monitor a variety of conditions.
In addition, the information provided by fundus imaging can also be used in research to better understand the underlying mechanisms of various eye conditions and as a non-invasive tool for visualization of the general microvascular circulation health and a direct view to part of the central nervous system. As such, the fundus image can serve as a window to systemic health.
The Human Phenotype Project (HPP) performs fundus imaging on each participant’s eyes to produce image files. To process and enhance the data, an open source software pipeline: AutoMorph: Automated Retinal Vascular Morphology Quantification via a Deep Learning Pipeline (Zhou 2022), that combines several different deep learning models is used. Specifically for the following steps: (1) Image pre-processing. (2) Image quality grading. (3) Anatomical segmentation (binary vessel segmentation, artery/vein segmentation, and optic disc segmentation). (4) Various morphological feature measurements such as vessel caliber, tortuosity density, fractal dimension etc. These features were calculated separately for segmented veins and arteries, and also as a combined feature. The current pipeline does not include automatic identification or clinical interpretation of eye abnormalities such as age-macular degeneration (AMD) or edema, glaucoma signs, microaneurysms etc’ that can be derived from the fundus image.
Data availability:
- All tabular information is stored in a main parquet file:
fundus.parquet - Derived microvasculature information is stored in a secondary parquet file:
microvasculature.parquet - Image files including segmentations are stored in subfolders and mapped in the parqet files.
pl = PhenoLoader('fundus')
plPhenoLoader for fundus with
76 fields
3 tables: ['fundus', 'microvasculature', '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 | ||||||||||||||||||||
| fundus_image_left | Fundus image (left) | Fundus image (left) | 3 | images | Image file (individual) | Primary | NaN | Single | string | .jpg | fundus/fundus.parquet | NaN | NaN | NaN | NaN | NaN | Accruing | Both sexes | 2021-02-17 | NaN |
| fundus_image_right | Fundus image (right) | Fundus image (right) | 3 | images | Image file (individual) | Primary | NaN | Single | string | .jpg | fundus/fundus.parquet | NaN | NaN | NaN | NaN | NaN | Accruing | Both sexes | 2021-02-17 | NaN |
| collection_date | Collection date (YYYY-MM-DD) | Collection date (YYYY-MM-DD) | 3 | fundus | Date | Collection time | NaN | Single | datetime64[ns] | NaN | fundus/fundus.parquet | NaN | NaN | NaN | NaN | NaN | Accruing | Both sexes | 2021-02-17 | NaN |
| timezone | Timezone | Timezone for timestamp columns | 3 | fundus | Categorical (single) | Collection time | 001_03 | Single | category | NaN | fundus/fundus.parquet | NaN | NaN | NaN | NaN | NaN | Accruing | Both sexes | 2021-02-17 | NaN |
| collection_timestamp | Collection timestamp | Collection timestamp | 3 | fundus | Datetime | Collection time | NaN | Single | datetime64[ns, Asia/Jerusalem] | NaN | fundus/fundus.parquet | NaN | NaN | NaN | NaN | NaN | Accruing | Both sexes | 2021-02-17 | NaN |
| device_software_version | Software version | Device software Version | 3 | fundus | Text | Auxiliary | NaN | Single | string | NaN | fundus/fundus.parquet | NaN | NaN | NaN | NaN | NaN | Accruing | Both sexes | 2021-02-17 | NaN |
| image_view_type_left | Fundus image view type (left) | Nasal or central view (left) | 3 | fundus | Categorical (single) | Auxiliary | 003_02 | Single | string | NaN | fundus/fundus.parquet | NaN | NaN | NaN | NaN | NaN | Accruing | Both sexes | 2021-02-17 | NaN |
| image_view_type_right | Fundus image view type (right) | Nasal or central view (right) | 3 | fundus | Categorical (single) | Auxiliary | 003_02 | Single | string | NaN | fundus/fundus.parquet | NaN | NaN | NaN | NaN | NaN | Accruing | Both sexes | 2021-02-17 | NaN |
| preprocessing_centre_width_left | preprocessing centre width (left) | preprocessing centre width (left) | 3 | images | Continuous | Supporting | NaN | Single | int | NaN | fundus/fundus.parquet | NaN | NaN | NaN | NaN | NaN | Accruing | Both sexes | 2021-02-17 | NaN |
| preprocessing_centre_height_left | preprocessing centre height (left) | preprocessing centre height (left) | 3 | images | Continuous | Supporting | NaN | Single | int | NaN | fundus/fundus.parquet | NaN | NaN | NaN | NaN | NaN | Accruing | Both sexes | 2021-02-17 | NaN |
| preprocessing_radius_left | preprocessing circle radius (left) | preprocessing circle radius (left) | 3 | images | Continuous | Supporting | NaN | Single | int | NaN | fundus/fundus.parquet | NaN | NaN | NaN | NaN | NaN | Accruing | Both sexes | 2021-02-17 | NaN |
| preprocessing_scale_resolution_left | preprocessing scale resolution (left) | preprocessing scale resolution (left) | 3 | images | Continuous | Supporting | NaN | Single | float | NaN | fundus/fundus.parquet | NaN | NaN | NaN | NaN | NaN | Accruing | Both sexes | 2021-02-17 | NaN |
| preprocessing_centre_width_right | preprocessing centre width (left) | preprocessing centre width (right) | 3 | images | Continuous | Supporting | NaN | Single | int | NaN | fundus/fundus.parquet | NaN | NaN | NaN | NaN | NaN | Accruing | Both sexes | 2021-02-17 | NaN |
| preprocessing_centre_height_right | preprocessing centre height (left) | preprocessing centre height (right) | 3 | images | Continuous | Supporting | NaN | Single | int | NaN | fundus/fundus.parquet | NaN | NaN | NaN | NaN | NaN | Accruing | Both sexes | 2021-02-17 | NaN |
| preprocessing_radius_right | preprocessing circle radius (left) | preprocessing circle radius (right) | 3 | images | Continuous | Supporting | NaN | Single | int | NaN | fundus/fundus.parquet | NaN | NaN | NaN | NaN | NaN | Accruing | Both sexes | 2021-02-17 | NaN |
| preprocessing_scale_resolution_right | preprocessing scale resolution (left) | preprocessing scale resolution (right) | 3 | images | Continuous | Supporting | NaN | Single | float | NaN | fundus/fundus.parquet | NaN | NaN | NaN | NaN | NaN | Accruing | Both sexes | 2021-02-17 | NaN |
| fundus_image_quality_prediction_right | Fundus image quality prediction (right) | Fundus image quality prediction (right) | 3 | images | Categorical (single) | Supporting | 003_01 | Single | category | NaN | fundus/fundus.parquet | NaN | NaN | NaN | NaN | NaN | Accruing | Both sexes | 2021-02-17 | NaN |
| fundus_image_quality_good_score_right | Fundus image quality good score (right) | Fundus image quality good score (right) | 3 | images | Continuous | Supporting | NaN | Single | float | NaN | fundus/fundus.parquet | NaN | NaN | NaN | NaN | NaN | Accruing | Both sexes | 2021-02-17 | NaN |
| fundus_image_quality_usable_score_right | Fundus image quality usable score (right) | Fundus image quality usable score (right) | 3 | images | Continuous | Supporting | NaN | Single | float | NaN | fundus/fundus.parquet | NaN | NaN | NaN | NaN | NaN | Accruing | Both sexes | 2021-02-17 | NaN |
| fundus_image_quality_bad_score_right | Fundus image quality bad score (right) | Fundus image quality bad score (right) | 3 | images | Continuous | Supporting | NaN | Single | float | NaN | fundus/fundus.parquet | NaN | NaN | NaN | NaN | NaN | Accruing | Both sexes | 2021-02-17 | NaN |
| fundus_image_quality_sd_good_right | Fundus image quality SD good (right) | Fundus image quality SD good (right) | 3 | images | Continuous | Supporting | NaN | Single | float | NaN | fundus/fundus.parquet | NaN | NaN | NaN | NaN | NaN | Accruing | Both sexes | 2021-02-17 | NaN |
| fundus_image_quality_sd_usable_right | Fundus image quality SD usable (right) | Fundus image quality SD usable (right) | 3 | images | Continuous | Supporting | NaN | Single | float | NaN | fundus/fundus.parquet | NaN | NaN | NaN | NaN | NaN | Accruing | Both sexes | 2021-02-17 | NaN |
| fundus_image_quality_sd_bad_right | Fundus image quality SD bad (right) | Fundus image quality SD bad (right) | 3 | images | Continuous | Supporting | NaN | Single | float | NaN | fundus/fundus.parquet | NaN | NaN | NaN | NaN | NaN | Accruing | Both sexes | 2021-02-17 | NaN |
| fundus_image_quality_prediction_left | Fundus image quality prediction (right) | Fundus image quality prediction (right) | 3 | images | Categorical (single) | Supporting | 003_01 | Single | category | NaN | fundus/fundus.parquet | NaN | NaN | NaN | NaN | NaN | Accruing | Both sexes | 2021-02-17 | NaN |
| fundus_image_quality_good_score_left | Fundus image quality good score (right) | Fundus image quality good score (right) | 3 | images | Continuous | Supporting | NaN | Single | float | NaN | fundus/fundus.parquet | NaN | NaN | NaN | NaN | NaN | Accruing | Both sexes | 2021-02-17 | NaN |
| fundus_image_quality_usable_score_left | Fundus image quality usable score (right) | Fundus image quality usable score (right) | 3 | images | Continuous | Supporting | NaN | Single | float | NaN | fundus/fundus.parquet | NaN | NaN | NaN | NaN | NaN | Accruing | Both sexes | 2021-02-17 | NaN |
| fundus_image_quality_bad_score_left | Fundus image quality bad score (right) | Fundus image quality bad score (right) | 3 | images | Continuous | Supporting | NaN | Single | float | NaN | fundus/fundus.parquet | NaN | NaN | NaN | NaN | NaN | Accruing | Both sexes | 2021-02-17 | NaN |
| fundus_image_quality_sd_good_left | Fundus image quality SD good (left) | Fundus image quality SD good (left) | 3 | images | Continuous | Supporting | NaN | Single | float | NaN | fundus/fundus.parquet | NaN | NaN | NaN | NaN | NaN | Accruing | Both sexes | 2021-02-17 | NaN |
| fundus_image_quality_sd_usable_left | Fundus image quality SD usable (left) | Fundus image quality SD usable (left) | 3 | images | Continuous | Supporting | NaN | Single | float | NaN | fundus/fundus.parquet | NaN | NaN | NaN | NaN | NaN | Accruing | Both sexes | 2021-02-17 | NaN |
| fundus_image_quality_sd_bad_left | Fundus image quality SD bad (left) | Fundus image quality SD bad (left) | 3 | images | Continuous | Supporting | NaN | Single | float | NaN | fundus/fundus.parquet | NaN | NaN | NaN | NaN | NaN | Accruing | Both sexes | 2021-02-17 | NaN |
| fundus_image_binary_artery_segmentation_left | Fundus image binary artery segmentation (left) | Fundus image binary artery segmentation (left) | 3 | segmented_images | Image file (individual) | Primary | NaN | Single | string | .jpg | fundus/microvasculature.parquet | NaN | NaN | NaN | NaN | NaN | Accruing | Both sexes | 2021-02-17 | NaN |
| fundus_image_binary_artery_segmentation_right | Fundus image binary artery segmentation (right) | Fundus image binary artery segmentation (right) | 3 | segmented_images | Image file (individual) | Primary | NaN | Single | string | .jpg | fundus/microvasculature.parquet | NaN | NaN | NaN | NaN | NaN | Accruing | Both sexes | 2021-02-17 | NaN |
| fundus_image_binary_vein_segmentation_left | Fundus image binary vein segmentation (left) | Fundus image binary vein segmentation (left) | 3 | segmented_images | Image file (individual) | Primary | NaN | Single | string | .jpg | fundus/microvasculature.parquet | NaN | NaN | NaN | NaN | NaN | Accruing | Both sexes | 2021-02-17 | NaN |
| fundus_image_binary_vein_segmentation_right | Fundus image binary vein segmentation (right) | Fundus image binary vein segmentation (right) | 3 | segmented_images | Image file (individual) | Primary | NaN | Single | string | .jpg | fundus/microvasculature.parquet | NaN | NaN | NaN | NaN | NaN | Accruing | Both sexes | 2021-02-17 | NaN |
| fundus_image_binary_artery_and_vein_classification_left | Fundus image binary artery and vein classifica... | Fundus image binary artery and vein classifica... | 3 | segmented_images | Image file (individual) | Primary | NaN | Single | string | .jpg | fundus/microvasculature.parquet | NaN | NaN | NaN | NaN | NaN | Accruing | Both sexes | 2021-02-17 | NaN |
| fundus_image_binary_artery_and_vein_classification_right | Fundus image binary artery and vein classifica... | Fundus image binary artery and vein classifica... | 3 | segmented_images | Image file (individual) | Primary | NaN | Single | string | .jpg | fundus/microvasculature.parquet | NaN | NaN | NaN | NaN | NaN | Accruing | Both sexes | 2021-02-17 | NaN |
| fundus_image_binary_vessel_segmentation_left | Fundus image binary vessel segmentation (left) | Fundus image binary vessel segmentation (left) | 3 | segmented_images | Image file (individual) | Primary | NaN | Single | string | .jpg | fundus/microvasculature.parquet | NaN | NaN | NaN | NaN | NaN | Accruing | Both sexes | 2021-02-17 | NaN |
| fundus_image_binary_vessel_segmentation_right | Fundus image binary vessel segmentation (right) | Fundus image binary vessel segmentation (right) | 3 | segmented_images | Image file (individual) | Primary | NaN | Single | string | .jpg | fundus/microvasculature.parquet | NaN | NaN | NaN | NaN | NaN | Accruing | Both sexes | 2021-02-17 | NaN |
| fractal_dimension_left | Fractal dimension (left) | Fractal dimension (left) | 3 | microvasculature | Continuous | Primary | NaN | Single | float | NaN | fundus/microvasculature.parquet | NaN | NaN | NaN | NaN | NaN | Accruing | Both sexes | 2021-02-17 | NaN |
| vessel_density_left | Vessel density (left) | Vessel density (left) | 3 | microvasculature | Continuous | Primary | NaN | Single | float | NaN | fundus/microvasculature.parquet | NaN | NaN | NaN | NaN | NaN | Accruing | Both sexes | 2021-02-17 | NaN |
| average_width_left | Average width (left) | Average width (left) | 3 | microvasculature | Continuous | Primary | NaN | Single | float | NaN | fundus/microvasculature.parquet | NaN | NaN | NaN | NaN | NaN | Accruing | Both sexes | 2021-02-17 | NaN |
| distance_tortuosity_left | Distance tortuosity (left) | Distance tortuosity (left) | 3 | microvasculature | Continuous | Primary | NaN | Single | float | NaN | fundus/microvasculature.parquet | NaN | NaN | NaN | NaN | NaN | Accruing | Both sexes | 2021-02-17 | NaN |
| squared_curvature_tortuosity_left | Squared curvature tortuosity (left) | Squared curvature tortuosity (left) | 3 | microvasculature | Continuous | Primary | NaN | Single | float | NaN | fundus/microvasculature.parquet | NaN | NaN | NaN | NaN | NaN | Accruing | Both sexes | 2021-02-17 | NaN |
| tortuosity_density_left | Tortuosity density (left) | Tortuosity density (left) | 3 | microvasculature | Continuous | Primary | NaN | Single | float | NaN | fundus/microvasculature.parquet | NaN | NaN | NaN | NaN | NaN | Accruing | Both sexes | 2021-02-17 | NaN |
| artery_fractal_dimension_left | Artery fractal dimension (left) | Artery fractal dimension (left) | 3 | microvasculature | Continuous | Primary | NaN | Single | float | NaN | fundus/microvasculature.parquet | NaN | NaN | NaN | NaN | NaN | Accruing | Both sexes | 2021-02-17 | NaN |
| artery_vessel_density_left | Artery vessel density (left) | Artery vessel density (left) | 3 | microvasculature | Continuous | Primary | NaN | Single | float | NaN | fundus/microvasculature.parquet | NaN | NaN | NaN | NaN | NaN | Accruing | Both sexes | 2021-02-17 | NaN |
| artery_average_width_left | Artery average width (left) | Artery average width (left) | 3 | microvasculature | Continuous | Primary | NaN | Single | float | NaN | fundus/microvasculature.parquet | NaN | NaN | NaN | NaN | NaN | Accruing | Both sexes | 2021-02-17 | NaN |
| artery_distance_tortuosity_left | Artery distance tortuosity (left) | Artery distance tortuosity (left) | 3 | microvasculature | Continuous | Primary | NaN | Single | float | NaN | fundus/microvasculature.parquet | NaN | NaN | NaN | NaN | NaN | Accruing | Both sexes | 2021-02-17 | NaN |
| artery_squared_curvature_tortuosity_left | Artery squared curvature tortuosity (left) | Artery squared curvature tortuosity (left) | 3 | microvasculature | Continuous | Primary | NaN | Single | float | NaN | fundus/microvasculature.parquet | NaN | NaN | NaN | NaN | NaN | Accruing | Both sexes | 2021-02-17 | NaN |
| artery_tortuosity_density_left | Artery tortuosity density (left) | Artery tortuosity density (left) | 3 | microvasculature | Continuous | Primary | NaN | Single | float | NaN | fundus/microvasculature.parquet | NaN | NaN | NaN | NaN | NaN | Accruing | Both sexes | 2021-02-17 | NaN |
| vein_fractal_dimension_left | Vein fractal dimension (left) | Vein fractal dimension (left) | 3 | microvasculature | Continuous | Primary | NaN | Single | float | NaN | fundus/microvasculature.parquet | NaN | NaN | NaN | NaN | NaN | Accruing | Both sexes | 2021-02-17 | NaN |
| vein_vessel_density_left | Vein vessel density (left) | Vein vessel density (left) | 3 | microvasculature | Continuous | Primary | NaN | Single | float | NaN | fundus/microvasculature.parquet | NaN | NaN | NaN | NaN | NaN | Accruing | Both sexes | 2021-02-17 | NaN |
| vein_average_width_left | Vein average width (left) | Vein average width (left) | 3 | microvasculature | Continuous | Primary | NaN | Single | float | NaN | fundus/microvasculature.parquet | NaN | NaN | NaN | NaN | NaN | Accruing | Both sexes | 2021-02-17 | NaN |
| vein_distance_tortuosity_left | Vein distance tortuosity (left) | Vein distance tortuosity (left) | 3 | microvasculature | Continuous | Primary | NaN | Single | float | NaN | fundus/microvasculature.parquet | NaN | NaN | NaN | NaN | NaN | Accruing | Both sexes | 2021-02-17 | NaN |
| vein_squared_curvature_tortuosity_left | Vein squared curvature tortuosity (left) | Vein squared curvature tortuosity (left) | 3 | microvasculature | Continuous | Primary | NaN | Single | float | NaN | fundus/microvasculature.parquet | NaN | NaN | NaN | NaN | NaN | Accruing | Both sexes | 2021-02-17 | NaN |
| vein_tortuosity_density_left | Vein tortuosity density (left) | Vein tortuosity density (left) | 3 | microvasculature | Continuous | Primary | NaN | Single | float | NaN | fundus/microvasculature.parquet | NaN | NaN | NaN | NaN | NaN | Accruing | Both sexes | 2021-02-17 | NaN |
| fractal_dimension_right | Fractal dimension (right) | Fractal dimension (right) | 3 | microvasculature | Continuous | Primary | NaN | Single | float | NaN | fundus/microvasculature.parquet | NaN | NaN | NaN | NaN | NaN | Accruing | Both sexes | 2021-02-17 | NaN |
| vessel_density_right | Vessel density (right) | Vessel density (right) | 3 | microvasculature | Continuous | Primary | NaN | Single | float | NaN | fundus/microvasculature.parquet | NaN | NaN | NaN | NaN | NaN | Accruing | Both sexes | 2021-02-17 | NaN |
| average_width_right | Average width (right) | Average width (right) | 3 | microvasculature | Continuous | Primary | NaN | Single | float | NaN | fundus/microvasculature.parquet | NaN | NaN | NaN | NaN | NaN | Accruing | Both sexes | 2021-02-17 | NaN |
| distance_tortuosity_right | Distance tortuosity (right) | Distance tortuosity (right) | 3 | microvasculature | Continuous | Primary | NaN | Single | float | NaN | fundus/microvasculature.parquet | NaN | NaN | NaN | NaN | NaN | Accruing | Both sexes | 2021-02-17 | NaN |
| squared_curvature_tortuosity_right | Squared curvature tortuosity (right) | Squared curvature tortuosity (right) | 3 | microvasculature | Continuous | Primary | NaN | Single | float | NaN | fundus/microvasculature.parquet | NaN | NaN | NaN | NaN | NaN | Accruing | Both sexes | 2021-02-17 | NaN |
| tortuosity_density_right | Tortuosity density (right) | Tortuosity density (right) | 3 | microvasculature | Continuous | Primary | NaN | Single | float | NaN | fundus/microvasculature.parquet | NaN | NaN | NaN | NaN | NaN | Accruing | Both sexes | 2021-02-17 | NaN |
| artery_fractal_dimension_right | Artery fractal dimension (right) | Artery fractal dimension (right) | 3 | microvasculature | Continuous | Primary | NaN | Single | float | NaN | fundus/microvasculature.parquet | NaN | NaN | NaN | NaN | NaN | Accruing | Both sexes | 2021-02-17 | NaN |
| artery_vessel_density_right | Artery vessel density (right) | Artery vessel density (right) | 3 | microvasculature | Continuous | Primary | NaN | Single | float | NaN | fundus/microvasculature.parquet | NaN | NaN | NaN | NaN | NaN | Accruing | Both sexes | 2021-02-17 | NaN |
| artery_average_width_right | Artery average width (right) | Artery average width (right) | 3 | microvasculature | Continuous | Primary | NaN | Single | float | NaN | fundus/microvasculature.parquet | NaN | NaN | NaN | NaN | NaN | Accruing | Both sexes | 2021-02-17 | NaN |
| artery_distance_tortuosity_right | Artery distance tortuosity (right) | Artery distance tortuosity (right) | 3 | microvasculature | Continuous | Primary | NaN | Single | float | NaN | fundus/microvasculature.parquet | NaN | NaN | NaN | NaN | NaN | Accruing | Both sexes | 2021-02-17 | NaN |
| artery_squared_curvature_tortuosity_right | Artery squared curvature tortuosity (right) | Artery squared curvature tortuosity (right) | 3 | microvasculature | Continuous | Primary | NaN | Single | float | NaN | fundus/microvasculature.parquet | NaN | NaN | NaN | NaN | NaN | Accruing | Both sexes | 2021-02-17 | NaN |
| artery_tortuosity_density_right | Artery tortuosity density (right) | Artery tortuosity density (right) | 3 | microvasculature | Continuous | Primary | NaN | Single | float | NaN | fundus/microvasculature.parquet | NaN | NaN | NaN | NaN | NaN | Accruing | Both sexes | 2021-02-17 | NaN |
| vein_fractal_dimension_right | Vein fractal dimension (right) | Vein fractal dimension (right) | 3 | microvasculature | Continuous | Primary | NaN | Single | float | NaN | fundus/microvasculature.parquet | NaN | NaN | NaN | NaN | NaN | Accruing | Both sexes | 2021-02-17 | NaN |
| vein_vessel_density_right | Vein vessel density (right) | Vein vessel density (right) | 3 | microvasculature | Continuous | Primary | NaN | Single | float | NaN | fundus/microvasculature.parquet | NaN | NaN | NaN | NaN | NaN | Accruing | Both sexes | 2021-02-17 | NaN |
| vein_average_width_right | Vein average width (right) | Vein average width (right) | 3 | microvasculature | Continuous | Primary | NaN | Single | float | NaN | fundus/microvasculature.parquet | NaN | NaN | NaN | NaN | NaN | Accruing | Both sexes | 2021-02-17 | NaN |
| vein_distance_tortuosity_right | Vein distance tortuosity (right) | Vein distance tortuosity (right) | 3 | microvasculature | Continuous | Primary | NaN | Single | float | NaN | fundus/microvasculature.parquet | NaN | NaN | NaN | NaN | NaN | Accruing | Both sexes | 2021-02-17 | NaN |
| vein_squared_curvature_tortuosity_right | Vein squared curvature tortuosity (right) | Vein squared curvature tortuosity (right) | 3 | microvasculature | Continuous | Primary | NaN | Single | float | NaN | fundus/microvasculature.parquet | NaN | NaN | NaN | NaN | NaN | Accruing | Both sexes | 2021-02-17 | NaN |
| vein_tortuosity_density_right | Vein tortuosity density (right) | Vein tortuosity density (right) | 3 | microvasculature | Continuous | Primary | NaN | Single | float | NaN | fundus/microvasculature.parquet | NaN | NaN | NaN | NaN | NaN | Accruing | Both sexes | 2021-02-17 | NaN |
Plot histogram and ecdf for vessel_density_left at baseline visit
from pheno_utils.basic_plots import hist_ecdf_plots
col = "vessel_density_left"
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 | |
|---|---|---|---|---|---|---|---|---|
| vessel_density_left | 4827.0 | 0.078963 | 0.006806 | 0.046615 | 0.074714 | 0.078946 | 0.083297 | 0.106708 |