OptiJ: Open-source optical projection tomography of large organ samples.
Journal
Scientific reports
ISSN: 2045-2322
Titre abrégé: Sci Rep
Pays: England
ID NLM: 101563288
Informations de publication
Date de publication:
30 10 2019
30 10 2019
Historique:
received:
19
06
2019
accepted:
09
10
2019
entrez:
1
11
2019
pubmed:
2
11
2019
medline:
2
11
2019
Statut:
epublish
Résumé
The three-dimensional imaging of mesoscopic samples with Optical Projection Tomography (OPT) has become a powerful tool for biomedical phenotyping studies. OPT uses visible light to visualize the 3D morphology of large transparent samples. To enable a wider application of OPT, we present OptiJ, a low-cost, fully open-source OPT system capable of imaging large transparent specimens up to 13 mm tall and 8 mm deep with 50 µm resolution. OptiJ is based on off-the-shelf, easy-to-assemble optical components and an ImageJ plugin library for OPT data reconstruction. The software includes novel correction routines for uneven illumination and sample jitter in addition to CPU/GPU accelerated reconstruction for large datasets. We demonstrate the use of OptiJ to image and reconstruct cleared lung lobes from adult mice. We provide a detailed set of instructions to set up and use the OptiJ framework. Our hardware and software design are modular and easy to implement, allowing for further open microscopy developments for imaging large organ samples.
Identifiants
pubmed: 31666606
doi: 10.1038/s41598-019-52065-0
pii: 10.1038/s41598-019-52065-0
pmc: PMC6821862
doi:
Types de publication
Journal Article
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Pagination
15693Subventions
Organisme : Biotechnology and Biological Sciences Research Council
ID : BB/R021805/1
Pays : United Kingdom
Organisme : RCUK | Biotechnology and Biological Sciences Research Council (BBSRC)
ID : BB/R021805/1
Pays : International
Organisme : Wellcome Trust
ID : 203249/Z/16/Z
Pays : United Kingdom
Organisme : Medical Research Council
ID : MR/K015850/1
Pays : United Kingdom
Organisme : Medical Research Council
ID : MR/K02292X/1
Pays : United Kingdom
Organisme : RCUK | Biotechnology and Biological Sciences Research Council (BBSRC)
ID : BB/P027431/1
Pays : International
Organisme : Wellcome Trust
ID : 089703/Z/09/Z
Pays : United Kingdom
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