title: SuRVoS: Super-Region Volume Segmentation workbench.
abstract: Segmentation of biological volumes is a crucial step needed to fully analyse their scientific content. Not having access to convenient tools with which to segment or annotate the data means many biological volumes remain under-utilised. Automatic segmentation of biological volumes is still a very challenging research field, and current methods usually require a large amount of manually-produced training data to deliver a high-quality segmentation. However, the complex appearance of cellular features and the high variance from one sample to another, along with the time-consuming work of manually labelling complete volumes, makes the required training data very scarce or non-existent. Thus, fully automatic approaches are often infeasible for many practical applications. With the aim of unifying the segmentation power of automatic approaches with the user expertise and ability to manually annotate biological samples, we present a new workbench named SuRVoS (Super-Region Volume Segmentation). Within this software, a volume to be segmented is first partitioned into hierarchical segmentation layers (named Super-Regions) and is then interactively segmented with the user's knowledge input in the form of training annotations. SuRVoS first learns from and then extends user inputs to the rest of the volume, while using Super-Regions for quicker and easier segmentation than when using a voxel grid. These benefits are especially noticeable on noisy, low-dose, biological datasets.
authors.affiliation: School of Computer Science, University of Nottingham, Jubilee Campus, Nottingham NG8 1BB, United Kingdom; Diamond Light Source, Harwell Science & Innovation Campus, Didcot OX11 0DE, United Kingdom. Electronic address: Imanol.Luengo@nottingham.ac.uk.
authors.forename: Imanol
authors.initials: I
authors.lastname: Luengo
authors.affiliation: Diamond Light Source, Harwell Science & Innovation Campus, Didcot OX11 0DE, United Kingdom. Electronic address: Michele.Darrow@diamond.ac.uk.
authors.forename: Michele C
authors.initials: MC
authors.lastname: Darrow
authors.affiliation: Diamond Light Source, Harwell Science & Innovation Campus, Didcot OX11 0DE, United Kingdom. Electronic address: Matthew.Spink@diamond.ac.uk.
authors.forename: Matthew C
authors.initials: MC
authors.lastname: Spink
authors.affiliation: Department of Biological Sciences, National University of Singapore, Singapore 117563, Singapore; National Center for Macromolecular Imaging, Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA. Electronic address: Ying.Sun@bcm.edu.
authors.forename: Ying
authors.initials: Y
authors.lastname: Sun
authors.affiliation: Department of Cell Biology and Neuroscience, and Center for Integrative Proteomics Research, Rutgers University, NJ 08901, USA. Electronic address: dai@biology.rutgers.edu.
authors.forename: Wei
authors.initials: W
authors.lastname: Dai
authors.affiliation: Department of Biological Sciences, National University of Singapore, Singapore 117563, Singapore. Electronic address: dbshyc@nus.edu.sg.
authors.forename: Cynthia Y
authors.initials: CY
authors.lastname: He
authors.affiliation: National Center for Macromolecular Imaging, Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA. Electronic address: Wah@bcm.edu.
authors.forename: Wah
authors.initials: W
authors.lastname: Chiu
authors.affiliation: School of Computer Science, University of Nottingham, Jubilee Campus, Nottingham NG8 1BB, United Kingdom. Electronic address: Tony.Pridmore@nottingham.ac.uk.
authors.forename: Tony
authors.initials: T
authors.lastname: Pridmore
authors.affiliation: Diamond Light Source, Harwell Science & Innovation Campus, Didcot OX11 0DE, United Kingdom. Electronic address: Alun.Ashton@diamond.ac.uk.
authors.forename: Alun W
authors.initials: AW
authors.lastname: Ashton
authors.affiliation: Diamond Light Source, Harwell Science & Innovation Campus, Didcot OX11 0DE, United Kingdom. Electronic address: Elizabeth.Duke@diamond.ac.uk.
authors.forename: Elizabeth M H
authors.initials: EMH
authors.lastname: Duke
authors.affiliation: Diamond Light Source, Harwell Science & Innovation Campus, Didcot OX11 0DE, United Kingdom. Electronic address: Mark.Basham@diamond.ac.uk.
authors.forename: Mark
authors.initials: M
authors.lastname: Basham
authors.affiliation: School of Computer Science, University of Nottingham, Jubilee Campus, Nottingham NG8 1BB, United Kingdom. Electronic address: Andrew.P.French@nottingham.ac.uk.
authors.forename: Andrew P
authors.initials: AP
authors.lastname: French
mesh_terms: D000465:Algorithms; D066289:Data Curation / Q000379:methods; D066264:Datasets as Topic; D000069550:Machine Learning; D012984:Software
keywords: Cryo electron tomography; Cryo soft X-ray tomography; Hierarchical segmentation; Interactive segmentation; Semi-supervised learning; Super-Regions