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Phenotypic profiling of high throughput imaging screens with generic deep convolutional features

Lookup NU author(s): Phillip Jackson, Professor Boguslaw ObaraORCiD


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© 2019 MVA Organization. While deep learning has seen many recent applications to drug discovery, most have focused on predicting activity or toxicity directly from chemical structure. Phenotypic changes exhibited in cellular images are also indications of the mechanism of action (MoA) of chemical compounds. In this paper, we show how pre-trained convolutional image features can be used to assist scientists in discovering interesting chemical clusters for further investigation. Our method reduces the dimensionality of raw fluorescent stained images from a high throughput imaging (HTI) screen, producing an embedding space that groups together images with similar cellular phenotypes. Running standard unsupervised clustering on this embedding space yields a set of distinct phenotypic clusters. This allows scientists to further select and focus on interesting clusters for downstream analyses. We validate the consistency of our embedding space qualitatively with t-sne visualizations, and quantitatively by measuring embedding variance among images that are known to be similar. Results suggested the usefulness of our proposed workflow using deep learning and clustering and it can lead to robust HTI screening and compound triage.

Publication metadata

Author(s): Jackson PT, Wang Y, Knight S, Chen H, Dorval T, Brown M, Bendtsen C, Obara B

Publication type: Conference Proceedings (inc. Abstract)

Publication status: Published

Conference Name: 16th International Conference on Machine Vision Applications (MVA 2019)

Year of Conference: 2019

Pages: 05-19

Online publication date: 11/07/2019

Acceptance date: 02/04/2018

Publisher: IEEE


DOI: 10.23919/MVA.2019.8757871

Library holdings: Search Newcastle University Library for this item

ISBN: 9784901122184