TY - JOUR

T1 - First automatic size measurements for the separation of dwarf birch and tree birch pollen in MIS 6 to MIS 1 records from Northern Germany

AU - Theuerkauf, Martin

AU - Nehring, Elias

AU - Gillert, Alexander

AU - Bodien, Philipp Morten

AU - Hein, Michael

AU - Urban, Brigitte

N1 - Publisher Copyright: © 2024 The Authors. Ecology and Evolution published by John Wiley & Sons Ltd.

PY - 2024/6/1

Y1 - 2024/6/1

N2 - During past glacial periods, the land cover of Northern Eurasia and North America repeatedly shifted between open steppe tundra and boreal/temperate forest. Tracking these changes and estimating the coverage of open versus forested vegetation in past glacial and interglacial landscapes is notoriously difficult because the characteristic dwarf birches of the tundra and the tree birches of the boreal and temperate forests produce similar pollen grains that are difficult to distinguish in the pollen record. One objective approach to separating dwarf birch pollen from tree birch pollen is to use grain size statistics. However, the required grain size measurements are time-consuming and, therefore, rarely produced. Here, we present an approach to automatic size measurement based on image recognition with convolutional neural networks and machine learning. It includes three main steps. First, the TOFSI algorithm is applied to detect and classify pollen, including birch pollen, in lake sediment samples. Second, a Resnet-18 neural network is applied to select the birch pollen suitable for measurement. Third, semantic segmentation is applied to detect the outline and the area and mean width of each detected birch pollen grain. Test applications with two pollen records from Northern Germany, one covering the Lateglacial-Early Holocene transition and the other covering the Mid to Late Pleistocene transition, show that the new technical approach is well suited to measure the area and mean width of birch pollen rapidly (>1000 per hour) and with high accuracy. Our new network-based tool facilitates more regular size measurements of birch pollen. Expanded analysis of modern birch pollen will help to better understand size variations in birch pollen between birch species and in response to environmental factors as well as differential sample preparation. Analysis of fossil samples will allow better quantification of dwarf birch versus tree birch in past environments.

AB - During past glacial periods, the land cover of Northern Eurasia and North America repeatedly shifted between open steppe tundra and boreal/temperate forest. Tracking these changes and estimating the coverage of open versus forested vegetation in past glacial and interglacial landscapes is notoriously difficult because the characteristic dwarf birches of the tundra and the tree birches of the boreal and temperate forests produce similar pollen grains that are difficult to distinguish in the pollen record. One objective approach to separating dwarf birch pollen from tree birch pollen is to use grain size statistics. However, the required grain size measurements are time-consuming and, therefore, rarely produced. Here, we present an approach to automatic size measurement based on image recognition with convolutional neural networks and machine learning. It includes three main steps. First, the TOFSI algorithm is applied to detect and classify pollen, including birch pollen, in lake sediment samples. Second, a Resnet-18 neural network is applied to select the birch pollen suitable for measurement. Third, semantic segmentation is applied to detect the outline and the area and mean width of each detected birch pollen grain. Test applications with two pollen records from Northern Germany, one covering the Lateglacial-Early Holocene transition and the other covering the Mid to Late Pleistocene transition, show that the new technical approach is well suited to measure the area and mean width of birch pollen rapidly (>1000 per hour) and with high accuracy. Our new network-based tool facilitates more regular size measurements of birch pollen. Expanded analysis of modern birch pollen will help to better understand size variations in birch pollen between birch species and in response to environmental factors as well as differential sample preparation. Analysis of fossil samples will allow better quantification of dwarf birch versus tree birch in past environments.

KW - automatic pollen recognition

KW - convolutional neural networks

KW - dwarf birch

KW - Holocene

KW - machine learning

KW - middle and upper Pleistocene

KW - TOFSI

KW - tree birch

KW - Biology

UR - http://www.scopus.com/inward/record.url?scp=85196216224&partnerID=8YFLogxK

UR - https://www.mendeley.com/catalogue/3bd2f036-ee9c-3f9b-a1ea-2e8304b4d47c/

U2 - 10.1002/ece3.11510

DO - 10.1002/ece3.11510

M3 - Journal articles

C2 - 38882530

AN - SCOPUS:85196216224

VL - 14

JO - Ecology and Evolution

JF - Ecology and Evolution

SN - 2045-7758

IS - 6

M1 - e11510

ER -