Document of bibliographic reference 329783

BibliographicReference record

Type

Bibliographic resource

Type of document

Journal article

BibLvlCode

AS

Title

Deep learning-based diatom taxonomy on virtual slides

Abstract

Deep convolutional neural networks are emerging as the state of the art method for supervised classification of images also in the context of taxonomic identification. Different morphologies and imaging technologies applied across organismal groups lead to highly specific image domains, which need customization of deep learning solutions. Here we provide an example using deep convolutional neural networks (CNNs) for taxonomic identification of the morphologically diverse microalgal group of diatoms. Using a combination of high-resolution slide scanning microscopy, web-based collaborative image annotation and diatom-tailored image analysis, we assembled a diatom image database from two Southern Ocean expeditions. We use these data to investigate the effect of CNN architecture, background masking, data set size and possible concept drift upon image classification performance. Surprisingly, VGG16, a relatively old network architecture, showed the best performance and generalizing ability on our images. Different from a previous study, we found that background masking slightly improved performance. In general, training only a classifier on top of convolutional layers pre-trained on extensive, but not domain-specific image data showed surprisingly high performance (F1 scores around 97%) with already relatively few (100–300) examples per class, indicating that domain adaptation to a novel taxonomic group can be feasible with a limited investment of effort.

WebOfScience code

https://www.webofscience.com/wos/woscc/full-record/WOS:000608581100001

Bibliographic citation

Kloster, M.; Langenkämper, D.; Zurowietz, M.; Beszteri, B.; Nattkemper, T.W. (2020). Deep learning-based diatom taxonomy on virtual slides. NPG Scientific Reports 10(1): 13 pp. https://dx.doi.org/10.1038/s41598-020-71165-w

Is peer reviewed

true

Access rights

open access

Is accessible for free

true