title: OpenSegSPIM: a user-friendly segmentation tool for SPIM data.
abstract: OpenSegSPIM is an open access and user friendly 3D automatic quantitative analysis tool for Single Plane Illumination Microscopy data. The software is designed to extract, in a user-friendly way, quantitative relevant information from SPIM image stacks, such as the number of nuclei or cells. It provides quantitative measurement (volume, sphericity, distance, intensity) on Light Sheet Fluorescent Microscopy images.
  
  
  
  freely available from http://www.opensegspim.weebly.com Source code and binaries under BSD License.
  
  
  
  lgole@imcb.a-star.edu.sg or wmyu@imcb.a-star.edu.sg or sohail.ahmed@imb.a-star.edu.sg
  
  
  
  Supplementary data are available at Bioinformatics online.
authors.affiliation: Institute of Medical Biology, Agency for Science, Technology and Research (A*STAR).
authors.forename: Laurent
authors.initials: L
authors.lastname: Gole
authors.affiliation: Institute of Molecular and Cell Biology, Agency for Science, Technology and Research (A*STAR).
authors.forename: Kok Haur
authors.initials: KH
authors.lastname: Ong
authors.affiliation: IPAL UMI 2955 (CNRS, UPMC, UJF, IMT, I2R, NUS), BioInformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), 13867, Singapore.
authors.forename: Thomas
authors.initials: T
authors.lastname: Boudier
authors.affiliation: Institute of Molecular and Cell Biology, Agency for Science, Technology and Research (A*STAR).
authors.forename: Weimiao
authors.initials: W
authors.lastname: Yu
authors.affiliation: Institute of Medical Biology, Agency for Science, Technology and Research (A*STAR).
authors.forename: Sohail
authors.initials: S
authors.lastname: Ahmed
mesh_terms: D000465:Algorithms; D000818:Animals; D002467:Cell Nucleus; D006801:Humans; D007090:Image Interpretation, Computer-Assisted; D008853:Microscopy; D012984:Software