2022 journal article

Forabot: Automated Planktic Foraminifera Isolation and Imaging

Geochemistry, Geophysics, Geosystems, 23(12).

Source: ORCID
Added: February 10, 2023

Physical inspection and sorting of foraminifera is a necessity in many research labs, as foraminifera serve as paleoenvironmental and chronostratigraphic indicators. In order to gain counts of species from samples, analyze chemical compositions, or extract morphological properties of foraminifera, research labs require human time and effort handling and sorting these microscopic fossils. The presented work describes Forabot, an open-source system which can physically manipulate individual foraminifera for imaging and isolation with minimal human interaction. The major components to build a Forabot are outlined in this work, with supplementary information available which allows for other researchers to build a Forabot with low-cost, off-the-shelf components. From a washed and sieved sample of hundreds of foraminifera, the Forabot is shown to be capable of isolating and imaging individual forams. The timing of the Forabot's current pipeline allows for the processing of up to 27 foram specimens per hour, a rate that can be improved for future classification purposes by reducing image quality and/or quantity. Along with the physical descriptions, the image processing and classification pipelines are also reviewed. A proof-of-concept classifier utilizes a finetuned VGG-16 network to achieve a classification accuracy of 79% on a validation set of foraminifera images collected with Forabot. In conclusion, the system is able to be built by researchers for a low cost, effectively manipulate foraminifera with few mistakes, provide quality images for future research, and classify the species of imaged forams.