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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




No version available



  • person_outline Pavel Tomančák

Publication for Stitching

Stitching citations


Oral Administration and Detection of a Near Infrared Molecular Imaging Agent in an Orthotopic Mouse Model for Breast Cancer Screening

Mol Pharm
PMCID: 5941251
PMID: 29696981
DOI: 10.1021/acs.molpharmaceut.7b00994
call_split See protocol

[…] . These slides were then washed in PBS and imaged on an Olympus FV1200 confocal microscope equipped with 405, 488, 543, 633, and 748 nm laser lines.The integrin image in was post processed to remove stitching artifacts (Figure S2). We used the ImageJ FFT bandpass filter, suppressing horizontal and vertical lines with a cutoff of 2500 pixels and 0 pixels with a 5% tolerance. […]


Concepts in Light Microscopy of Viruses

PMCID: 5923496
PMID: 29670029
DOI: 10.3390/v10040202

[…] entation 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 of new […]


GABAergic inhibition in dual transmission cholinergic and GABAergic striatal interneurons is abolished in Parkinson disease

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

[…] 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” plugi […]


Retention and Functional Effect of Adipose Derived Stromal Cells Administered in Alginate Hydrogel in a Rat Model of Acute Myocardial Infarction

PMCID: 5892231
PMID: 29765421
DOI: 10.1155/2018/7821461
call_split See protocol

[…] hematoxylin and eosin (H&E). Prior to antibody staining, antigen retrieval was performed using citrate buffer and microwave treatment. Images were obtained by an ×20 objective scanning and subsequent stitching, producing images of the entire short axis slice. Fibrosis on Masson's trichrome stainings was quantified using ImageJ (Fiji) on the entire heart. CD31 clusters in peri-infarct regions were […]


Projections of the Diencephalospinal Dopaminergic System to Peripheral Sense Organs in Larval Zebrafish (Danio rerio)

Front Neuroanat
PMCID: 5868122
PMID: 29615872
DOI: 10.3389/fnana.2018.00020
call_split See protocol

[…] rast 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). […]


A modular, open source, slide scanning microscope for diagnostic applications in resource constrained settings

PLoS One
PMCID: 5854341
PMID: 29543835
DOI: 10.1371/journal.pone.0194063
call_split See protocol

[…] erforming 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 in […]


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

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