from pheno_utils import PhenoLoader3-fundus
3 - fundus
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 (Figure 1). 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.
All tabular information is stored in a main parquet file: fundus.parquet Image files including segmentations are stored in subfolders and mapped in the main parqet file.
dl = PhenoLoader('fundus', age_sex_dataset=None)
dlDataLoader for fundus with
76 fields
1 tables: ['fundus']dl.dict| field_string | description_string | parent_dataframe | relative_location | value_type | units | sampling_rate | item_type | array | cohorts | data_type | debut | pandas_dtype | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| tabular_field_name | |||||||||||||
| fundus_image_left | Fundus image (left) | Fundus image (left) | NaN | fundus.parquet | Text | None | NaN | Bulk | Single | 10K | image | 2021-02-17 | string |
| fundus_image_right | Fundus image (right) | Fundus image (right) | NaN | fundus.parquet | Text | None | NaN | Bulk | Single | 10K | image | 2021-02-17 | string |
| collection_date | Collection date (YYYY-MM-DD) | Collection date (YYYY-MM-DD) | NaN | fundus.parquet | Date | Time | NaN | Data | Single | 10K | tabular | 2021-02-17 | datetime64[ns] |
| timezone | Timezone | Timezone for timestamp columns | NaN | fundus.parquet | NaN | NaN | NaN | NaN | NaN | NaN | NaN | NaN | string |
| collection_timestamp | Collection timestamp | Collection timestamp | NaN | fundus.parquet | NaN | Time | NaN | Data | Single | 10K | tabular | NaN | datetime64[ns, Asia/Jerusalem] |
| device_software_version | Software version | Device software Version | NaN | fundus.parquet | NaN | NaN | NaN | Data | Single | 10K | tabular | NaN | string |
| image_view_type_left | Fundus image view type (left) | Nasal or central view | NaN | fundus.parquet | Categorical (multiple) | Text | NaN | Data | Single | 10K | tabular | 2021-02-17 | string |
| image_view_type_right | Fundus image view type (right) | Nasal or central view | NaN | fundus.parquet | Categorical (multiple) | Text | NaN | Data | Single | 10K | tabular | 2021-02-17 | string |
| preprocessing_centre_width_left | preprocessing centre width (left) | preprocessing centre width (left) | NaN | fundus.parquet | Continuous | Boolean | NaN | Data | Single | 10K | tabular | 2021-02-17 | float |
| preprocessing_centre_height_left | preprocessing centre height (left) | preprocessing centre height (left) | NaN | fundus.parquet | Continuous | Boolean | NaN | Data | Single | 10K | tabular | 2021-02-17 | float |
| preprocessing_radius_left | preprocessing circle radius (left) | preprocessing circle radius (left) | NaN | fundus.parquet | Continuous | Boolean | NaN | Data | Single | 10K | tabular | 2021-02-17 | float |
| preprocessing_scale_resolution_left | preprocessing scale resolution (left) | preprocessing scale resolution (left) | NaN | fundus.parquet | Continuous | Boolean | NaN | Data | Single | 10K | tabular | 2021-02-17 | float |
| preprocessing_centre_width_right | preprocessing centre width (left) | preprocessing centre width (right) | NaN | fundus.parquet | Continuous | Boolean | NaN | Data | Single | 10K | tabular | 2021-02-17 | float |
| preprocessing_centre_height_right | preprocessing centre height (left) | preprocessing centre height (right) | NaN | fundus.parquet | Continuous | Boolean | NaN | Data | Single | 10K | tabular | 2021-02-17 | float |
| preprocessing_radius_right | preprocessing circle radius (left) | preprocessing circle radius (right) | NaN | fundus.parquet | Continuous | Boolean | NaN | Data | Single | 10K | tabular | 2021-02-17 | float |
| preprocessing_scale_resolution_right | preprocessing scale resolution (left) | preprocessing scale resolution (right) | NaN | fundus.parquet | Continuous | Boolean | NaN | Data | Single | 10K | tabular | 2021-02-17 | float |
| fundus_image_quality_prediction_right | Fundus image quality prediction (right) | Fundus image quality prediction (right) | NaN | fundus.parquet | Continuous | Boolean | NaN | Data | Single | 10K | tabular | 2021-02-17 | category |
| fundus_image_quality_good_score_right | Fundus image quality good score (right) | Fundus image quality good score (right) | NaN | fundus.parquet | Continuous | Probability | NaN | Data | Single | 10K | tabular | 2021-02-17 | float |
| fundus_image_quality_usable_score_right | Fundus image quality usable score (right) | Fundus image quality usable score (right) | NaN | fundus.parquet | Continuous | Probability | NaN | Data | Single | 10K | tabular | 2021-02-17 | float |
| fundus_image_quality_bad_score_right | Fundus image quality bad score (right) | Fundus image quality bad score (right) | NaN | fundus.parquet | Continuous | Probability | NaN | Data | Single | 10K | tabular | 2021-02-17 | float |
| fundus_image_quality_sd_good_right | Fundus image quality SD good (right) | Fundus image quality SD good (right) | NaN | fundus.parquet | Continuous | Probability | NaN | Data | Single | 10K | tabular | 2021-02-17 | float |
| fundus_image_quality_sd_usable_right | Fundus image quality SD usable (right) | Fundus image quality SD usable (right) | NaN | fundus.parquet | Continuous | Probability | NaN | Data | Single | 10K | tabular | 2021-02-17 | float |
| fundus_image_quality_sd_bad_right | Fundus image quality SD bad (right) | Fundus image quality SD bad (right) | NaN | fundus.parquet | Continuous | Probability | NaN | Data | Single | 10K | tabular | 2021-02-17 | float |
| fundus_image_quality_prediction_left | Fundus image quality prediction (right) | Fundus image quality prediction (right) | NaN | fundus.parquet | Continuous | Boolean | NaN | Data | Single | 10K | tabular | 2021-02-17 | category |
| fundus_image_quality_good_score_left | Fundus image quality good score (right) | Fundus image quality good score (right) | NaN | fundus.parquet | Continuous | Probability | NaN | Data | Single | 10K | tabular | 2021-02-17 | float |
| fundus_image_quality_usable_score_left | Fundus image quality usable score (right) | Fundus image quality usable score (right) | NaN | fundus.parquet | Continuous | Probability | NaN | Data | Single | 10K | tabular | 2021-02-17 | float |
| fundus_image_quality_bad_score_left | Fundus image quality bad score (right) | Fundus image quality bad score (right) | NaN | fundus.parquet | Continuous | Probability | NaN | Data | Single | 10K | tabular | 2021-02-17 | float |
| fundus_image_quality_sd_good_left | Fundus image quality SD good (left) | Fundus image quality SD good (left) | NaN | fundus.parquet | Continuous | Probability | NaN | Data | Single | 10K | tabular | 2021-02-17 | float |
| fundus_image_quality_sd_usable_left | Fundus image quality SD usable (left) | Fundus image quality SD usable (left) | NaN | fundus.parquet | Continuous | Probability | NaN | Data | Single | 10K | tabular | 2021-02-17 | float |
| fundus_image_quality_sd_bad_left | Fundus image quality SD bad (left) | Fundus image quality SD bad (left) | NaN | fundus.parquet | Continuous | Probability | NaN | Data | Single | 10K | tabular | 2021-02-17 | float |
| fundus_image_binary_artery_segmentation_left | Fundus image binary artery segmentation (left) | Fundus image binary artery segmentation (left) | NaN | fundus.parquet | Text | None | NaN | Bulk | Single | 10K | image | 2021-02-17 | string |
| fundus_image_binary_artery_segmentation_right | Fundus image binary artery segmentation (right) | Fundus image binary artery segmentation (right) | NaN | fundus.parquet | Text | None | NaN | Bulk | Single | 10K | image | 2021-02-17 | string |
| fundus_image_binary_vein_segmentation_left | Fundus image binary vein segmentation (left) | Fundus image binary vein segmentation (left) | NaN | fundus.parquet | Text | None | NaN | Bulk | Single | 10K | image | 2021-02-17 | string |
| fundus_image_binary_vein_segmentation_right | Fundus image binary vein segmentation (right) | Fundus image binary vein segmentation (right) | NaN | fundus.parquet | Text | None | NaN | Bulk | Single | 10K | image | 2021-02-17 | string |
| fundus_image_binary_artery_and_vein_classification_left | Fundus image binary artery and vein classifica... | Fundus image binary artery and vein classifica... | NaN | fundus.parquet | Text | None | NaN | Bulk | Single | 10K | image | 2021-02-17 | string |
| fundus_image_binary_artery_and_vein_classification_right | Fundus image binary artery and vein classifica... | Fundus image binary artery and vein classifica... | NaN | fundus.parquet | Text | None | NaN | Bulk | Single | 10K | image | 2021-02-17 | string |
| fundus_image_binary_vessel_segmentation_left | Fundus image binary vessel segmentation (left) | Fundus image binary vessel segmentation (left) | NaN | fundus.parquet | Text | None | NaN | Bulk | Single | 10K | image | 2021-02-17 | string |
| fundus_image_binary_vessel_segmentation_right | Fundus image binary vessel segmentation (right) | Fundus image binary vessel segmentation (right) | NaN | fundus.parquet | Text | None | NaN | Bulk | Single | 10K | image | 2021-02-17 | string |
| fractal_dimension_left | Fractal dimension (left) | Fractal dimension (left) | NaN | fundus.parquet | Continuous | None | NaN | Data | Single | 10K | tabular | 2021-02-17 | float |
| vessel_density_left | Vessel density (left) | Vessel density (left) | NaN | fundus.parquet | Continuous | density | NaN | Data | Single | 10K | tabular | 2021-02-17 | float |
| average_width_left | Average width (left) | Average width (left) | NaN | fundus.parquet | Continuous | pixels | NaN | Data | Single | 10K | tabular | 2021-02-17 | float |
| distance_tortuosity_left | Distance tortuosity (left) | Distance tortuosity (left) | NaN | fundus.parquet | Continuous | None | NaN | Data | Single | 10K | tabular | 2021-02-17 | float |
| squared_curvature_tortuosity_left | Squared curvature tortuosity (left) | Squared curvature tortuosity (left) | NaN | fundus.parquet | Continuous | None | NaN | Data | Single | 10K | tabular | 2021-02-17 | float |
| tortuosity_density_left | Tortuosity density (left) | Tortuosity density (left) | NaN | fundus.parquet | Continuous | density | NaN | Data | Single | 10K | tabular | 2021-02-17 | float |
| artery_fractal_dimension_left | Artery fractal dimension (left) | Artery fractal dimension (left) | NaN | fundus.parquet | Continuous | None | NaN | Data | Single | 10K | tabular | 2021-02-17 | float |
| artery_vessel_density_left | Artery vessel density (left) | Artery vessel density (left) | NaN | fundus.parquet | Continuous | density | NaN | Data | Single | 10K | tabular | 2021-02-17 | float |
| artery_average_width_left | Artery average width (left) | Artery average width (left) | NaN | fundus.parquet | Continuous | pixels | NaN | Data | Single | 10K | tabular | 2021-02-17 | float |
| artery_distance_tortuosity_left | Artery distance tortuosity (left) | Artery distance tortuosity (left) | NaN | fundus.parquet | Continuous | None | NaN | Data | Single | 10K | tabular | 2021-02-17 | float |
| artery_squared_curvature_tortuosity_left | Artery squared curvature tortuosity (left) | Artery squared curvature tortuosity (left) | NaN | fundus.parquet | Continuous | None | NaN | Data | Single | 10K | tabular | 2021-02-17 | float |
| artery_tortuosity_density_left | Artery tortuosity density (left) | Artery tortuosity density (left) | NaN | fundus.parquet | Continuous | density | NaN | Data | Single | 10K | tabular | 2021-02-17 | float |
| vein_fractal_dimension_left | Vein fractal dimension (left) | Vein fractal dimension (left) | NaN | fundus.parquet | Continuous | None | NaN | Data | Single | 10K | tabular | 2021-02-17 | float |
| vein_vessel_density_left | Vein vessel density (left) | Vein vessel density (left) | NaN | fundus.parquet | Continuous | density | NaN | Data | Single | 10K | tabular | 2021-02-17 | float |
| vein_average_width_left | Vein average width (left) | Vein average width (left) | NaN | fundus.parquet | Continuous | pixels | NaN | Data | Single | 10K | tabular | 2021-02-17 | float |
| vein_distance_tortuosity_left | Vein distance tortuosity (left) | Vein distance tortuosity (left) | NaN | fundus.parquet | Continuous | None | NaN | Data | Single | 10K | tabular | 2021-02-17 | float |
| vein_squared_curvature_tortuosity_left | Vein squared curvature tortuosity (left) | Vein squared curvature tortuosity (left) | NaN | fundus.parquet | Continuous | None | NaN | Data | Single | 10K | tabular | 2021-02-17 | float |
| vein_tortuosity_density_left | Vein tortuosity density (left) | Vein tortuosity density (left) | NaN | fundus.parquet | Continuous | density | NaN | Data | Single | 10K | tabular | 2021-02-17 | float |
| fractal_dimension_right | Fractal dimension (right) | Fractal dimension (right) | NaN | fundus.parquet | Continuous | None | NaN | Data | Single | 10K | tabular | 2021-02-17 | float |
| vessel_density_right | Vessel density (right) | Vessel density (right) | NaN | fundus.parquet | Continuous | density | NaN | Data | Single | 10K | tabular | 2021-02-17 | float |
| average_width_right | Average width (right) | Average width (right) | NaN | fundus.parquet | Continuous | pixels | NaN | Data | Single | 10K | tabular | 2021-02-17 | float |
| distance_tortuosity_right | Distance tortuosity (right) | Distance tortuosity (right) | NaN | fundus.parquet | Continuous | None | NaN | Data | Single | 10K | tabular | 2021-02-17 | float |
| squared_curvature_tortuosity_right | Squared curvature tortuosity (right) | Squared curvature tortuosity (right) | NaN | fundus.parquet | Continuous | None | NaN | Data | Single | 10K | tabular | 2021-02-17 | float |
| tortuosity_density_right | Tortuosity density (right) | Tortuosity density (right) | NaN | fundus.parquet | Continuous | density | NaN | Data | Single | 10K | tabular | 2021-02-17 | float |
| artery_fractal_dimension_right | Artery fractal dimension (right) | Artery fractal dimension (right) | NaN | fundus.parquet | Continuous | None | NaN | Data | Single | 10K | tabular | 2021-02-17 | float |
| artery_vessel_density_right | Artery vessel density (right) | Artery vessel density (right) | NaN | fundus.parquet | Continuous | density | NaN | Data | Single | 10K | tabular | 2021-02-17 | float |
| artery_average_width_right | Artery average width (right) | Artery average width (right) | NaN | fundus.parquet | Continuous | pixels | NaN | Data | Single | 10K | tabular | 2021-02-17 | float |
| artery_distance_tortuosity_right | Artery distance tortuosity (right) | Artery distance tortuosity (right) | NaN | fundus.parquet | Continuous | None | NaN | Data | Single | 10K | tabular | 2021-02-17 | float |
| artery_squared_curvature_tortuosity_right | Artery squared curvature tortuosity (right) | Artery squared curvature tortuosity (right) | NaN | fundus.parquet | Continuous | None | NaN | Data | Single | 10K | tabular | 2021-02-17 | float |
| artery_tortuosity_density_right | Artery tortuosity density (right) | Artery tortuosity density (right) | NaN | fundus.parquet | Continuous | density | NaN | Data | Single | 10K | tabular | 2021-02-17 | float |
| vein_fractal_dimension_right | Vein fractal dimension (right) | Vein fractal dimension (right) | NaN | fundus.parquet | Continuous | None | NaN | Data | Single | 10K | tabular | 2021-02-17 | float |
| vein_vessel_density_right | Vein vessel density (right) | Vein vessel density (right) | NaN | fundus.parquet | Continuous | density | NaN | Data | Single | 10K | tabular | 2021-02-17 | float |
| vein_average_width_right | Vein average width (right) | Vein average width (right) | NaN | fundus.parquet | Continuous | pixels | NaN | Data | Single | 10K | tabular | 2021-02-17 | float |
| vein_distance_tortuosity_right | Vein distance tortuosity (right) | Vein distance tortuosity (right) | NaN | fundus.parquet | Continuous | None | NaN | Data | Single | 10K | tabular | 2021-02-17 | float |
| vein_squared_curvature_tortuosity_right | Vein squared curvature tortuosity (right) | Vein squared curvature tortuosity (right) | NaN | fundus.parquet | Continuous | None | NaN | Data | Single | 10K | tabular | 2021-02-17 | float |
| vein_tortuosity_density_right | Vein tortuosity density (right) | Vein tortuosity density (right) | NaN | fundus.parquet | Continuous | density | NaN | Data | Single | 10K | tabular | 2021-02-17 | float |