OpenSPIM statistics

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Citations per year

Number of citations per year for the bioinformatics software tool OpenSPIM

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OpenSPIM specifications


Unique identifier OMICS_10786
Name OpenSPIM
Software type Package/Module
Interface Graphical user interface
Restrictions to use None
Operating system Unix/Linux
Programming languages Java
Computer skills Medium
Stability Stable
Maintained Yes


No version available

Publication for OpenSPIM

OpenSPIM citations


UbasM: An effective balanced optical clearing method for intact biomedical imaging

Sci Rep
PMCID: 5610269
PMID: 28939860
DOI: 10.1038/s41598-017-12484-3

[…] Observation was performed with a home-built OpenSPIM system equipped with a 10 × objective lens (Olympus LMPLFLN, NA = 0.25, WD = 21 mm). Cleared agarose-embedded samples were positioned under a 4D stage in front of the objective in the mountin […]


Automatic and adaptive heterogeneous refractive index compensation for light sheet microscopy

Nat Commun
PMCID: 5606987
PMID: 28931809
DOI: 10.1038/s41467-017-00514-7

[…] All samples were mounted to a custom pipette tip mount, inspired by previous work from Zeiss Microscopy, OpenSPIM, and OpenSPIN for our specific imaging chamber and RSSM, . The end of the pipette tip was plugged with RIMS and 1% agar and a small amount of cyanoacrylate glue holds the tissue specimen in p […]


4 dimensional functional profiling in the convulsant treated larval zebrafish brain

Sci Rep
PMCID: 5529444
PMID: 28747660
DOI: 10.1038/s41598-017-06646-6

[…] 40 pixels, 4 × 4 binning, 40 ms exposure, Andor, Belfast, Northern Ireland) to capture images. The camera and rotational axis (Picard Instruments, Albion, USA) were controlled though μManager and the OpenSPIM plugin. The Point Spread Function (PSF) of our system was determined by performing Z-stacks of 50 × 0.5 µm fluorescent beads, embedded in 1% agarose within a glass capillary. Images were acqu […]


Light sheet microscopy for slide free non destructive pathology of large clinical specimens

PMCID: 5940348
PMID: 29750130
DOI: 10.1038/s41551-017-0084

[…] ges when viewed with moderate- to high-NA microscope objectives. Finally, light-sheet microscopy systems can be simple and relatively inexpensive to build, as demonstrated by us and others (e.g., the OpenSPIM project) [].In summary, camera-based tissue-microscopy approaches (e.g., SIM and MUSE) are fast, but generally provide poor imaging depth (background suppression), which limits their effectiv […]


A novel imaging method for correlating 2D light microscopic data and 3D volume data based on block face imaging

Sci Rep
PMCID: 5473845
PMID: 28623366
DOI: 10.1038/s41598-017-03900-9

[…] including a cryostat, fluorescent microscope and personal computer, would cost approximately US$115250 (Supplementary Table ), which is more expensive than self-made light sheet microscope (US$57000; OpenSPIM), and less expensive than commercial light sheet microscope (US$260000), µCT (US$200000–1 million), MRI ($1 million per Tesla of magnetic field), and SEM for ATUM specimens (US$200000–600000) […]


NicoLase—An open source diode laser combiner, fiber launch, and sequencing controller for fluorescence microscopy

PLoS One
PMCID: 5354410
PMID: 28301563
DOI: 10.1371/journal.pone.0173879

[…] by sharing these implementations the hope is that downstream users can take advantage of these materials without having to reinvent the fiber launch, so to speak. In the same vein as projects such as OpenSPIM [], this provides a starting point for others who are encouraged to share their own improvements and modifications.Two generations of this project are presented. The first, referred to as the […]

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OpenSPIM institution(s)
Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany

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