Stitching protocols

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Stitching specifications


Unique identifier OMICS_25528
Name Stitching
Software type Application/Script
Interface Graphical user interface
Restrictions to use None
Operating system Unix/Linux, Mac OS
Programming languages Java
License GNU General Public License version 2.0
Computer skills Medium
Version 3.1.3
Stability Stable
Maintained Yes



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  • person_outline Pavel Tomančák <>

Publication for Stitching

Stitching in pipelines

PMCID: 5740639
PMID: 29162696
DOI: 10.1073/pnas.1706281114

[…] and then these points are connected with traces following the image intensity. is a maximal intensity projection of four stacks acquired separately and stitched together using fiji’s pairwise stitching plug-in (). the data shown in and were cropped from stacks following illumination correction using cidre () and deconvolution using huygens. since the illumination model is dictated […]

PMCID: 4769224
PMID: 26919712
DOI: 10.1371/journal.pone.0150170

[…] excitation imaging was performed on a prairie technologies ultima iv imaging system at loci., image stacks from the ultima iv were stitched together using the default settings in the grid/collection stitching plug-in for imagej that is distributed as part of the fiji project []. background subtraction was performed on both channels using the imagej subtract background function with a rolling […]

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Stitching in publications

PMCID: 5923496
PMID: 29670029
DOI: 10.3390/v10040202

[…] of imagej which is expanded by many plugins, as well as an integrated updating system and developer tools []. several plugins perform surprisingly complex tasks at high quality, including 3d stitching [], generation of super-resolution images from diffraction limited image stacks [], or lineage tracing []., while imagej/fiji provides a powerful and simple to use toolbox, the creation […]

PMCID: 5897332
PMID: 29651049
DOI: 10.1038/s41467-018-03802-y

[…] step of 0.50 μm., only neurons with a complete dendritic arbor were analyzed. stacks were imported in the open-source platform fiji ( and stitched together ( without any additional pre-processing, dendrite and axon reconstructions, as well as morphological metric measurements were performed using the semi-automated “simple neurite tracer” […]

PMCID: 5868122
PMID: 29615872
DOI: 10.3389/fnana.2018.00020

[…] and intensity of individual channels were linearly adjusted, and z-projections of subsets of focal planes or movies were generated. selected confocal tile scans were stitched using the “pairwise stitching” plug-in for imagej (preibisch et al., ). figures were assembled using inkscape (version 0.91, and photoshop (version 13.0, adobe cs6)., recently, zebrafish posterior […]

PMCID: 5854341
PMID: 29543835
DOI: 10.1371/journal.pone.0194063

[…] measurements on a regular rectangular grid (even if that grid contains many blank images), was both simpler and more effective., to mosaic the images together, we make use of the open source “stitching” plug-in included as part of the imagej distribution fiji []. image mosaicking programs typically operate by blending the edges of multiple images together, where the mosaicked sub-images […]

PMCID: 5809486
PMID: 29472841
DOI: 10.3389/fnmol.2018.00019

[…] size: 0.5 × 0.5 μm; z step size: 1.5 μm). all images were processed using imagej (schneider et al., ). tiled stacks were stitched using either the imaging software zen 2010 or the imagej plugin “stitching 2d/3d” (preibisch et al., ). subsequently, images were cropped to the same size and reduced to the same slice number. next, background fluorescence was reduced by subtracting […]

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

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