Forabot: Automated Planktic Foraminifera Isolation and Imaging
Abstract 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 forami...
| Main Authors: | , , , , , |
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| Format: | Article |
| Language: | English |
| Published: |
Wiley
2022-12-01
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| Series: | Geochemistry, Geophysics, Geosystems |
| Subjects: | |
| Online Access: | https://doi.org/10.1029/2022GC010689 |
| _version_ | 1797638029020495872 |
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| author | Turner Richmond Jeremy Cole Gabriella Dangler Michael Daniele Thomas Marchitto Edgar Lobaton |
| author_facet | Turner Richmond Jeremy Cole Gabriella Dangler Michael Daniele Thomas Marchitto Edgar Lobaton |
| author_sort | Turner Richmond |
| collection | DOAJ |
| description | Abstract 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. |
| first_indexed | 2024-03-11T12:56:47Z |
| format | Article |
| id | doaj.art-b27495c1118c418283f7460030dddce2 |
| institution | Directory Open Access Journal |
| issn | 1525-2027 |
| language | English |
| last_indexed | 2024-03-11T12:56:47Z |
| publishDate | 2022-12-01 |
| publisher | Wiley |
| record_format | Article |
| series | Geochemistry, Geophysics, Geosystems |
| spelling | doaj.art-b27495c1118c418283f7460030dddce22023-11-03T17:00:34ZengWileyGeochemistry, Geophysics, Geosystems1525-20272022-12-012312n/an/a10.1029/2022GC010689Forabot: Automated Planktic Foraminifera Isolation and ImagingTurner Richmond0Jeremy Cole1Gabriella Dangler2Michael Daniele3Thomas Marchitto4Edgar Lobaton5Department of Electrical and Computer Engineering North Carolina State University Raleigh NC USADepartment of Electrical and Computer Engineering North Carolina State University Raleigh NC USADepartment of Electrical and Computer Engineering North Carolina State University Raleigh NC USADepartment of Electrical and Computer Engineering North Carolina State University Raleigh NC USAInstitute of Arctic and Alpine Research University of Colorado Boulder CO USADepartment of Electrical and Computer Engineering North Carolina State University Raleigh NC USAAbstract 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.https://doi.org/10.1029/2022GC010689foraminiferaautomationclassification |
| spellingShingle | Turner Richmond Jeremy Cole Gabriella Dangler Michael Daniele Thomas Marchitto Edgar Lobaton Forabot: Automated Planktic Foraminifera Isolation and Imaging Geochemistry, Geophysics, Geosystems foraminifera automation classification |
| title | Forabot: Automated Planktic Foraminifera Isolation and Imaging |
| title_full | Forabot: Automated Planktic Foraminifera Isolation and Imaging |
| title_fullStr | Forabot: Automated Planktic Foraminifera Isolation and Imaging |
| title_full_unstemmed | Forabot: Automated Planktic Foraminifera Isolation and Imaging |
| title_short | Forabot: Automated Planktic Foraminifera Isolation and Imaging |
| title_sort | forabot automated planktic foraminifera isolation and imaging |
| topic | foraminifera automation classification |
| url | https://doi.org/10.1029/2022GC010689 |
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