Z-Spacing protocols

View Z-Spacing computational protocol

Z-Spacing statistics

To access cutting-edge analytics on consensus tools, life science contexts and associated fields, you will need to subscribe to our premium service.

Subscribe
info

Citations per year

Citations chart
info

Popular tool citations

chevron_left Image enhancement Image enhancement Serial block face imaging 3D reconstruction 3D image reconstruction chevron_right
Popular tools chart
info

Tool usage distribution map

Tool usage distribution map
info

Associated diseases

Associated diseases

Z-Spacing specifications

Information


Unique identifier OMICS_14438
Name Z-Spacing
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages Java
License GNU General Public License version 2.0
Computer skills Advanced
Stability Stable
Maintained Yes

Download


Versioning


Add your version

Documentation


Maintainer


  • person_outline Stephan Saalfeld <>

Publication for Z-Spacing

Z-Spacing in pipelines

 (4)
2015
PMCID: 4565980
PMID: 26312502
DOI: 10.7554/eLife.07759.019

[…] plan apochromat 100×/1.4 psf oil immersion objective lens was used, with liquid-cooled photometrics evolve em-ccd cameras for each channel. 15 images per section per channel were acquired with a z-spacing of 0.125 µm (; ). structured illumination reconstruction and wavelength alignment was completed using the softworx (ge healthcare) program. 3d image rendering and analysis was performed […]

2013
PMCID: 3587839
PMID: 23460676
DOI: 10.1083/jcb.201207024

[…] 100×/1.45 na oil objective lens, an em-ccd camera [cascade ii; photometrics], and metamorph 7.7.2 software [molecular devices]) was used (, , , , and ). for each picture, a stack with a z spacing of 0.2 µm was taken and deconvolved using the multidimensional deconvolution software huygens (scientific volume imaging). 3d reconstructions used imaris software (bitplane). […]

2012
PMCID: 3340615
PMID: 22538615
DOI: 10.1038/nature11012

[…] imaging. a plane of deep anaesthesia was maintained using a mixture of isofluorane gas and oxygen delivered via a nosecone. image stacks of 15 optical sections with a 400 um field of view and 3 μm z spacing were acquired every 30s for 60 – 80 minutes. the two-photon laser was tuned to a wavelength of 850 nm. volocity software (improvision) was used to create quicktime formatted movies of image […]

2009
PMCID: 2806478
PMID: 19995948
DOI: 10.1084/jem.20091586

[…] with a 20×/0.75 plan apochromat objective. a thermostated chamber (carl zeiss, inc.) was used to keep the microscope, mouse, tray, and objective at 37°c during the experiment. z-stacks (with 1-µm z-spacing) were acquired on the ventral skin (at least seven z-stacks per mouse, 0.22 mm2/z-stack), and the number of langerin-gfp+ cells per square millimeter was determined., skin from langerin-gfp […]


To access a full list of citations, you will need to upgrade to our premium service.

Z-Spacing in publications

 (200)
PMCID: 5946799
PMID: 29760998
DOI: 10.1364/BOE.9.002418

[…] light sheet. the bead size was chosen to be similar to the size of rbcs, to make the experimental scenario as similar as possible to real blood-flow images., frame pairs were selected at a chosen z spacing of δz (simulating out-of-plane motion of distance δz), and the second frame in each pair was synthetically shifted by 24 pixels (simulating in-plane motion of approximately 7 μm or one […]

PMCID: 5897341
PMID: 29651146
DOI: 10.1038/s41598-018-24283-5

[…] tooth pair positions from opposite sides in the four jaw quadrants of three specimens revealed a degree of bilateral symmetry in replacement pattern. reconstruction of zahnreihen yields an avergae z-spacing of 2.58 with simultaneous front-to-back tooth replacement. our study presents the earliest evidence of derived neoceratopsian traits of the complex dental batteries in ceratopsids. […]

PMCID: 5904847
PMID: 29696143
DOI: 10.3389/fcell.2018.00042

[…] for 15 min, then followed by the next cycle of decoding hybridization., cells were imaged under a nikon ti-e epofluorescence microscope equipped with a 100x objective, using a 5 μm range and 0.3 μm z spacing. images were captured using a coolsnap hq2 camera and nis-elements imaging software. chroma filters 49004 and 49009 were used for quasar 579 and cy5, respectively., fluorescent spots […]

PMCID: 5853029
PMID: 29540156
DOI: 10.1186/s12859-018-2087-4

[…] of the u2os cancer cells with hoechst stain from the image set bbbc006v1 [] from the broad bioimage benchmark collection [12]. this dataset consists of 32 images of each field of view with 2 μm z-spacing, 696 × 520 image size, 2× binning and 20× magnification. we then synthetically defocused the in-focus images by applying a convolution with the following point spread function evaluated […]

PMCID: 5832775
PMID: 29497176
DOI: 10.1038/s41598-018-22301-0

[…] \,\frac{1}{\frac{d3}{d1}}$$\end{document}p=1−vscaffoldvcube=1−π4∗1d2d1∗1d3d1where p is the porosity, d1 the diameter of the printed filament, d2 the filament xy spacing and d3 the z spacing, as is shown in fig. ., changes in scaffold topography were analyzed on a microscale with sem (jeol 6000) and on a nanoscale with atomic force microscopy (afm) (park xe-70). for the afm […]


To access a full list of publications, you will need to upgrade to our premium service.

Z-Spacing institution(s)
HHMI Janelia Research Campus, Ashburn, VA, USA
Z-Spacing funding source(s)
This work has been supported by a University of Texas at Arlington Phi Sigma Society Grant and NSF DDIG grants (NSF DEB-1501886 and NSF DEB-1501747).

Z-Spacing reviews

star_border star_border star_border star_border star_border
star star star star star

Be the first to review Z-Spacing