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Image5D specifications


Unique identifier OMICS_25926
Name Image5D
Software type Package/Module
Interface Graphical user interface
Restrictions to use None
Operating system Windows
Programming languages Java
Computer skills Medium
Version 1.1.6
Stability Stable
Maintained Yes




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  • person_outline Joachim Walter

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Image5D citations


A global Staphylococcus aureus proteome resource applied to the in vivo characterization of host pathogen interactions

Sci Rep
PMCID: 5591248
PMID: 28887440
DOI: 10.1038/s41598-017-10059-w

[…] in parallel by light microscopy. the pictures obtained were processed using fiji ( deltavision files were first adjusted for brightness and contrast and then prepared using the “image5d z/tp montage function”. afterwards, a non-destructive scale bar was added to all slices. the time-stamper plug-in allowed labeling of observation time for all slices. finally, the movies […]


Organization of olfactory centres in the malaria mosquito Anopheles gambiae

Nat Commun
PMCID: 5063964
PMID: 27694947
DOI: 10.1038/ncomms13010

[…] and manually inspected as to the overlap of orco and cd8 channels., to quantify orco (red) and mcd8-gfp (blue) co-staining with gfp fluorescence (green) in the larvae (), we used imagej with the image5d plugin and zen zeiss software to mark and count cells in each of the three fluorescence channels., to quantify the overlap of orco staining (red) and endogenous gfp fluorescence (green) […]


aPKC regulates apical localization of Lgl to restrict elongation of microridges in developing zebrafish epidermis

Nat Commun
PMCID: 4895443
PMID: 27249668
DOI: 10.1038/ncomms11643

[…] , , , , , , . zeiss lsm 710 was used for capturing movies with higher temporal resolution using acquisition speed of two frames per minute and played at a rate of 6 frames per second for , , , . the image5d plug-in from imagej was used for image processing and analysis of live movies., imaging conditions were kept uniform across most of the experiments. occasionally, pmt gains were slightly […]


Cause and Consequence of Tethering a SubTAD to Different Nuclear Compartments

Mol Cell
PMCID: 4747903
PMID: 26833089
DOI: 10.1016/j.molcel.2016.01.001

[…] 25th) per experiment. per condition we plot the average of this signal as taken from two independent biological replicates., fish was performed as described previously and detailed in the . imagej (image5d plugin) software was used to score touching (no unstained pixel in between fish signals) and nontouching (with unstained pixel(s) in between) alleles., p.j.w., p.h.l.k., and y.z. performed […]


Quantitative framework for ordered degradation of APC/C substrates

BMC Biol
PMCID: 4647693
PMID: 26573515
DOI: 10.1186/s12915-015-0205-6

[…] proliferating on the slide for 40–60 min in a 30 °c incubator prior to imaging., to quantify gfp intensity at each time point, we first used imagej ( [] and its plugin image5d ( to average across each z-stack and flatten it to 2d. gfp intensity was then quantified using matlab (the mathworks inc.) code previously […]


Multiple mechanisms determine the order of APC/C substrate degradation in mitosis

PMCID: 4195823
PMID: 25287299
DOI: 10.1083/jcb.201402041

[…] intensity and exposure time to generate fluorescent signals that were minimally sufficient for quantification., to quantify gfp intensity at each time point, we first used imagej () and its plugin image5d ( to average across each z stack and flatten it to 2d. gfp intensity was then quantified using matlab (the mathworks, inc.) code previously […]

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