Laurent Gole1, Kok Haur Ong2, Thomas Boudier3, Weimiao Yu2, Sohail Ahmed1. 1. Institute of Medical Biology, Agency for Science, Technology and Research (A*STAR). 2. Institute of Molecular and Cell Biology, Agency for Science, Technology and Research (A*STAR). 3. IPAL UMI 2955 (CNRS, UPMC, UJF, IMT, I2R, NUS), BioInformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), 13867, Singapore.
Abstract
UNLABELLED: 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. AVAILABILITY AND IMPLEMENTATION: freely available from http://www.opensegspim.weebly.com Source code and binaries under BSD License. CONTACT: lgole@imcb.a-star.edu.sg or wmyu@imcb.a-star.edu.sg or sohail.ahmed@imb.a-star.edu.sg SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
UNLABELLED: 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. AVAILABILITY AND IMPLEMENTATION: freely available from http://www.opensegspim.weebly.com Source code and binaries under BSD License. CONTACT: lgole@imcb.a-star.edu.sg or wmyu@imcb.a-star.edu.sg or sohail.ahmed@imb.a-star.edu.sg SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
Authors: Tuomas Kaseva; Bahareh Omidali; Eero Hippeläinen; Teemu Mäkelä; Ulla Wilppu; Alexey Sofiev; Arto Merivaara; Marjo Yliperttula; Sauli Savolainen; Eero Salli Journal: BMC Bioinformatics Date: 2022-07-21 Impact factor: 3.307