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.


Citations per year

Citations chart

Popular tool citations

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

Tool usage distribution map

Tool usage distribution map

Associated diseases

Associated diseases

Z-Spacing specifications


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



Add your version



  • person_outline Stephan Saalfeld <>

Publication for Z-Spacing

Z-Spacing in pipelines

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 […]

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). […]

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 […]

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

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