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. 2025 Mar 1;15(1):7312.
doi: 10.1038/s41598-025-91821-3.

Development of a new software for pore measurements in foraminifera and the constraints of pore proxy under high oxygen conditions

Rohan Subba  1 , Anupam Ghosh  2 , Rinku Kumar Mittal  3 , Sahina Gazi  4
Affiliations

Development of a new software for pore measurements in foraminifera and the constraints of pore proxy under high oxygen conditions

Rohan Subba et al. Sci Rep. .

Abstract

The rise in anthropogenic activities has significantly increased nutrient input into coastal habitats, such as lagoons and estuaries. This has led to increased eutrophication, which has considerably decreased the oxygen concentration in the aquatic systems. The pore patterns in benthic foraminifera have become a reliable proxy for accurately estimating the changes in these past oxygen conditions. However, there is currently no specific platform for a proxy study that can adequately quantify these pore structures and meet the requirements for pore image analysis in foraminifera. This study presents the new indigenously developed software MicroFoss42, specifically tailored for the pore morphometrics in foraminifera. It integrates computer vision and artificial intelligence to seamlessly extract the pore data from the images. Here, we demonstrate its use in measuring the pore count, diameter, area and circularity index of Ammonia parkinsoniana. Our results agree with the manual analysis, differing by less than 7.5%. This semi-automated software is designed to facilitate rapid analysis of the pore patterns in any foraminiferal species without the need for any prior datasets for training. Moreover, this study shows that the practical application of foraminiferal pore proxy in high oxygen conditions may be constrained.

Keywords: Benthic foraminifera; Computer vision; Dissolved oxygen; MicroFoss42; Pores.

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Conflict of interest statement

Declarations. Competing interests: The authors declare no competing interests.

Figures

Fig. 1
Fig. 1
The relationship between the pore parameters and DO (mg/L) (a–d). The calculated pore data is based on the new and manual method used in the study.
Fig. 1
Fig. 1
The relationship between the pore parameters and DO (mg/L) (a–d). The calculated pore data is based on the new and manual method used in the study.
Fig. 2
Fig. 2
Confusion matrix showing the relation between the pore data and measured environmental conditions. Pore data is based on the new method from the study.
Fig. 3
Fig. 3
The map shows the sample collection sites at Chilika Lagoon. A total of 37 locations were considered for the study. The colour bar represents the range of dissolved oxygen measured. This figure was produced using CorelDRAW X7 17.0.0.491 (https://www.coreldraw.com/en/).
Fig. 4
Fig. 4
Scanning electron microscope (SEM) images of pore pattern in Ammonia parkinsoniana from Chilika Lagoon (Odisha, India). The penultimate chamber (n-1) of the dorsal (spiral) side has been considered for the study.
Fig. 5
Fig. 5
Pore image analysis and data acquisition using MicroFoss42.
See this image and copyright information in PMC

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