Visual Search of Neuropil-Enriched RNAs from Brain In Situ Hybridization Data through the Image Analysis Pipeline Hippo-ATESC

Roberto Ugolotti 1 Pablo Mesejo 1 Samantha Zongaro 2 Barbara Bardoni 2 Gaia Berto 3 Federico Bianchi 3 Ivan Molineris 3 Mario Giacobini 3, 4 Stefano Cagnoni 1
1 Intelligent Bio-Inspired Systems lab (IBISlab)
2 UNS - Université Nice Sophia Antipolis
3 Molecular Biotechnology Center
4 Department of Veterinary Sciences
Abstract : Motivation: RNA molecules specifically enriched in the neuropil of neuronal cells and in particular in dendritic spines are of great interest for neurobiology in virtue of their involvement in synaptic structure and plasticity. The systematic recognition of such molecules is therefore a very important task. High resolution images of RNA in situ hybridization experiments contained in the Allen Brain Atlas (ABA) represent a very rich resource to identify them and have been so far exploited for this task through human-expert analysis. However, software tools that may automatically address the same objective are not very well developed. Results: In this study we describe an automatic method for exploring in situ hybridization data and discover neuropil-enriched RNAs in the mouse hippocampus. We called it Hippo-ATESC (Automatic Texture Extraction from the Hippocampal region using Soft Computing). Bioinformatic validation showed that the Hippo-ATESC is very efficient in the recognition of RNAs which are manually identified by expert curators as neuropil-enriched on the same image series. Moreover, we show that our method can also highlight genes revealed by microdissection-based methods but missed by human visual inspection. We experimentally validated our approach by identifying a non-coding transcript enriched in mouse synaptosomes. The code is freely available on the web at http://ibislab.ce.unipr.it/software/hippo/.
Keywords : Hippocampus Localization Image Segmentation Deformable Models Soft Computing Differential Evolution Image Registration Genetic Algorithms Feature Selection
Type de document :
Article dans une revue
PLoS ONE, Public Library of Science, 2013, 8 (9), 〈10.1371/journal.pone.0074481〉
Liste complète des métadonnées

Littérature citée [48 références]  Voir  Masquer  Télécharger
https://hal.inria.fr/hal-01221314
Contributeur : Pablo Mesejo Santiago <>
Soumis le : mardi 27 octobre 2015 - 16:57:40
Dernière modification le : vendredi 12 janvier 2018 - 11:02:41
Document(s) archivé(s) le : jeudi 28 janvier 2016 - 11:14:51

Fichier

journal.pone.0074481.pdf
Fichiers produits par l'(les) auteur(s)

Identifiants

Collections

UNICE | UNIV-COTEDAZUR

Citation

Roberto Ugolotti, Pablo Mesejo, Samantha Zongaro, Barbara Bardoni, Gaia Berto, et al.. Visual Search of Neuropil-Enriched RNAs from Brain In Situ Hybridization Data through the Image Analysis Pipeline Hippo-ATESC. PLoS ONE, Public Library of Science, 2013, 8 (9), 〈10.1371/journal.pone.0074481〉. 〈hal-01221314〉

Exporter

BibTeX TEI DC DCterms EndNote

Partager

Métriques

Consultations de la notice

112

Téléchargements de fichiers

48

Contact


archive-ouverte@inria.fr