title: A Robust Actin Filaments Image Analysis Framework.
abstract: The cytoskeleton is a highly dynamical protein network that plays a central role in numerous cellular physiological processes, and is traditionally divided into three components according to its chemical composition, i.e. actin, tubulin and intermediate filament cytoskeletons. Understanding the cytoskeleton dynamics is of prime importance to unveil mechanisms involved in cell adaptation to any stress type. Fluorescence imaging of cytoskeleton structures allows analyzing the impact of mechanical stimulation in the cytoskeleton, but it also imposes additional challenges in the image processing stage, such as the presence of imaging-related artifacts and heavy blurring introduced by (high-throughput) automated scans. However, although there exists a considerable number of image-based analytical tools to address the image processing and analysis, most of them are unfit to cope with the aforementioned challenges. Filamentous structures in images can be considered as a piecewise composition of quasi-straight segments (at least in some finer or coarser scale). Based on this observation, we propose a three-steps actin filaments extraction methodology: (i) first the input image is decomposed into a 'cartoon' part corresponding to the filament structures in the image, and a noise/texture part, (ii) on the 'cartoon' image, we apply a multi-scale line detector coupled with a (iii) quasi-straight filaments merging algorithm for fiber extraction. The proposed robust actin filaments image analysis framework allows extracting individual filaments in the presence of noise, artifacts and heavy blurring. Moreover, it provides numerous parameters such as filaments orientation, position and length, useful for further analysis. Cell image decomposition is relatively under-exploited in biological images processing, and our study shows the benefits it provides when addressing such tasks. Experimental validation was conducted using publicly available datasets, and in osteoblasts grown in two different conditions: static (control) and fluid shear stress. The proposed methodology exhibited higher sensitivity values and similar accuracy compared to state-of-the-art methods.
authors.affiliation: Electronics and Informatics Dept (ETRO), AVSP Lab, Vrije Universiteit Brussel, Brussels, Belgium.|VUB-EPFL International Joint Research Group (IJRG) NanoBiotechnology and NanoMedicine (NANO), Brussels, Belgium.
authors.forename: Mitchel
authors.initials: M
authors.lastname: Alioscha-Perez
authors.affiliation: VUB-EPFL International Joint Research Group (IJRG) NanoBiotechnology and NanoMedicine (NANO), Brussels, Belgium.|Laboratoire de Physique de la Matière Vivante (LPMV), EPFL, Cubotron, Lausanne, Switzerland.
authors.forename: Carine
authors.initials: C
authors.lastname: Benadiba
authors.affiliation: VUB-EPFL International Joint Research Group (IJRG) NanoBiotechnology and NanoMedicine (NANO), Brussels, Belgium.|Department of Bioengineering Sciences (DBIT), Vrije Universiteit Brussel, Brussels, Belgium.
authors.forename: Katty
authors.initials: K
authors.lastname: Goossens
authors.affiliation: VUB-EPFL International Joint Research Group (IJRG) NanoBiotechnology and NanoMedicine (NANO), Brussels, Belgium.|Laboratoire de Physique de la Matière Vivante (LPMV), EPFL, Cubotron, Lausanne, Switzerland.
authors.forename: Sandor
authors.initials: S
authors.lastname: Kasas
authors.affiliation: VUB-EPFL International Joint Research Group (IJRG) NanoBiotechnology and NanoMedicine (NANO), Brussels, Belgium.|Laboratoire de Physique de la Matière Vivante (LPMV), EPFL, Cubotron, Lausanne, Switzerland.
authors.forename: Giovanni
authors.initials: G
authors.lastname: Dietler
authors.affiliation: VUB-EPFL International Joint Research Group (IJRG) NanoBiotechnology and NanoMedicine (NANO), Brussels, Belgium.|Department of Bioengineering Sciences (DBIT), Vrije Universiteit Brussel, Brussels, Belgium.
authors.forename: Ronnie
authors.initials: R
authors.lastname: Willaert
authors.affiliation: Electronics and Informatics Dept (ETRO), AVSP Lab, Vrije Universiteit Brussel, Brussels, Belgium.|VUB-EPFL International Joint Research Group (IJRG) NanoBiotechnology and NanoMedicine (NANO), Brussels, Belgium.|Interuniversity Microelectronics Centre (IMEC), Heverlee, Belgium.
authors.forename: Hichem
authors.initials: H
authors.lastname: Sahli
mesh_terms: D000199:Actins / Q000032:analysis* / Q000737:chemistry* / Q000378:metabolism; D000465:Algorithms; D000818:Animals; D002460:Cell Line; D003599:Cytoskeleton / Q000737:chemistry* / Q000378:metabolism; D007091:Image Processing, Computer-Assisted / Q000379:methods*; D051379:Mice; D008856:Microscopy, Fluorescence; D013314:Stress, Mechanical
chemical_list: D000199:Actins