Using image segmentation models to analyse high-resolution earth observation data: new tools to monitor disease risks in changing environments

• Published in: International journal of health geographics Vol. 23; no. 1; p. 13
• Main Authors: Trujillano, Fedra, Jimenez, Gabriel, Manrique, Edgar, Kahamba, Najat F, Okumu, Fredros, Apollinaire, Nombre, Carrasco-Escobar, Gabriel, Barrett, Brian, Fornace, Kimberly
• Format: Journal Article
• Language: English
• Published: England BioMed Central Ltd 19.05.2024; BioMed Central; BMC
• Subjects: Analysis; Animals; Anopheles; Aquatic insects; Buildings; Care and treatment; Changing environments; Classification; Climate Change; Control programs; Creeks & streams; Datasets; Dengue fever; Diagnosis; Digitization; Disease control; Drone; Drone aircraft; Drones; Environmental changes; Epidemiology; Geographic Information Systems; Geospatial data; Health risks; Health surveillance; High resolution; Human settlements; Humans; Image acquisition; Image processing; Image Processing, Computer-Assisted - methods; Image resolution; Image segmentation; Infectious diseases; Labeling; Land cover; Land settlement; Malaria; Malaria - epidemiology; Medical imaging; Methodology; Methods; Mosquito Vectors; Mosquito-borne diseases; Mosquitoes; Performance assessment; Performance evaluation; Rain and rainfall; Rainfall; Remote sensing; Remote Sensing Technology - methods; Risk factors; Rural areas; Satellites; Seasons; Segment anything model; Software; Spatial data; UAV; Unmanned aerial vehicles; Vector-borne diseases; Water; Côte d'Ivoire; Malaysia; Tanzania; Singapore; South America; Southeast Asia; Peru; Africa; Mosquito-borne diseases; Drone; UAV; Remote sensing; Segment anything model
• ISSN: 1476-072X; 1476-072X
• DOI: 10.1186/s12942-024-00371-w

In the near future, the incidence of mosquito-borne diseases may expand to new sites due to changes in temperature and rainfall patterns caused by climate change. Therefore, there is a need to use recent technological advances to improve vector surveillance methodologies. Unoccupied Aerial Vehicles (UAVs), often called drones, have been used to collect high-resolution imagery to map detailed information on mosquito habitats and direct control measures to specific areas. Supervised classification approaches have been largely used to automatically detect vector habitats. However, manual data labelling for model training limits their use for rapid responses. Open-source foundation models such as the Meta AI Segment Anything Model (SAM) can facilitate the manual digitalization of high-resolution images. This pre-trained model can assist in extracting features of interest in a diverse range of images. Here, we evaluated the performance of SAM through the Samgeo package, a Python-based wrapper for geospatial data, as it has not been applied to analyse remote sensing images for epidemiological studies. We tested the identification of two land cover classes of interest: water bodies and human settlements, using different UAV acquired imagery across five malaria-endemic areas in Africa, South America, and Southeast Asia. We employed manually placed point prompts and text prompts associated with specific classes of interest to guide the image segmentation and assessed the performance in the different geographic contexts. An average Dice coefficient value of 0.67 was obtained for buildings segmentation and 0.73 for water bodies using point prompts. Regarding the use of text prompts, the highest Dice coefficient value reached 0.72 for buildings and 0.70 for water bodies. Nevertheless, the performance was closely dependent on each object, landscape characteristics and selected words, resulting in varying performance. Recent models such as SAM can potentially assist manual digitalization of imagery by vector control programs, quickly identifying key features when surveying an area of interest. However, accurate segmentation still requires user-provided manual prompts and corrections to obtain precise segmentation. Further evaluations are necessary, especially for applications in rural areas.