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Automatic Counting of Intra-Cellular Ribonucleo-Protein Aggregates in Saccharomyces cerevisiae Using a Textural Approach

Published online by Cambridge University Press:  13 February 2019

Ambroise Marin ,
Emmanuel Denimal ,
Lucie Bertheau ,
Stéphane Guyot ,
Ludovic Journaux  and
Paul Molin
Ambroise Marin*
Affiliation:
Agrosup, 26 boulevard docteur, petitjean, Dijon, Bourgogne, 21000, France
Emmanuel Denimal
Affiliation:
Agrosup, 26 boulevard docteur, petitjean, Dijon, Bourgogne, 21000, France
Lucie Bertheau
Affiliation:
Agrosup, 26 boulevard docteur, petitjean, Dijon, Bourgogne, 21000, France
Stéphane Guyot
Affiliation:
UMR A 02.102 Procédés Alimentaires et Microbiologiques, équipe Procédés Microbiologiques et Biotechnologiques, Agrosup Dijon/Université de Bourgogne, 1, esplanade Erasme, Dijon, Bourgogne 21000, France
Ludovic Journaux
Affiliation:
Agrosup, 26 boulevard docteur, petitjean, Dijon, Bourgogne, 21000, France Laboratoire d'Informatique de Bourgogne, EA7534, Université de Bourgogne, UFR Sciences et Techniques, allée Alain Savary, Dijon, Bourgogne, 21000, France
Paul Molin
Affiliation:
UMR A 02.102 Procédés Alimentaires et Microbiologiques, équipe Procédés Microbiologiques et Biotechnologiques, Agrosup Dijon/Université de Bourgogne, 1, esplanade Erasme, Dijon, Bourgogne, France
*
*Author for correspondence: Ambroise Marin, E-mail: ambroise.marin@agrosupdijon.fr
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Abstract

In the context of microbiology, recent studies show the importance of ribonucleo-protein aggregates (RNPs) for the understanding of mechanisms involved in cell responses to specific environmental conditions. The assembly and disassembly of aggregates is a dynamic process, the characterization of the stage of their evolution can be performed by the evaluation of their number. The aim of this study is to propose a method to automatically determine the count of RNPs. We show that the determination of a precise count is an issue by itself and hence, we propose three textural approaches: a classical point of view using Haralick features, a frequency point of view with generalized Fourier descriptors, and a structural point of view with Zernike moment descriptors (ZMD). These parameters are then used as inputs for a supervised classification in order to determine the most relevant. An experiment using a specific Saccharomyces cerevisiae strain presenting a fusion between a protein found in RNPs (PAB1) and the green fluorescent protein was performed to benchmark this approach. The fluorescence was observed with two-photon fluorescence microscopy. Results show that the textural approach, by mixing ZMD with Haralick features, allows for the characterization of the number of RNPs.

Keywords

Generalized Fourier descriptorsHaralickribonucleo-protein aggregatessub-cellular structuresZernike
Type
Biological Science Applications
Information
Microscopy and Microanalysis , Volume 25 , Issue 1 , February 2019 , pp. 164 - 179
Copyright
Copyright © Microscopy Society of America 2019 

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