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BioImageXD specifications


Unique identifier OMICS_13519
Name BioImageXD
Software type Package/Module
Interface Graphical user interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages C++, Python
License GNU General Public License version 2.0
Computer skills Medium
Version 1.0
Stability Stable
Maintained Yes




No version available

Publication for BioImageXD

BioImageXD citations


Development of image analysis software for quantification of viable cells in microchips

PLoS One
PMCID: 5832319
PMID: 29494694
DOI: 10.1371/journal.pone.0193605

[…] ed quickly [].There are many options for open access image analysis, originally developed to solve the needs of particular cases that were subsequently extended for other purposes, such as ImageJ [], BioImageXD [], Icy [], Fiji [], Vaa3D [], CellProfiler [], 3D Slicer [], Image Slicer [], Reconstruct [], FluoRender [], ImageSurfer [], OsiriX [], and IMOD [] among others [].There are also several a […]


A high content image analysis approach for quantitative measurements of chemosensitivity in patient derived tumor microtissues

Sci Rep
PMCID: 5529420
PMID: 28747710
DOI: 10.1038/s41598-017-06544-x

[…] a more focused approach to a particular problem, these software applications generally sacrifice some of the user-friendliness for the sake of increased customizability. Also the open-source software BioimageXD maintains a high repertoire of readily available tools, but is not ready for fast analysis of large image sets. Another solution for high-throughput image analysis, AMIDA, has been develope […]


Macrophages, but not neutrophils, are critical for proliferation of Burkholderia cenocepacia and ensuing host damaging inflammation

PLoS Pathog
PMCID: 5501683
PMID: 28651010
DOI: 10.1371/journal.ppat.1006437

[…] h image J (see specific details in movie legends). To quantify phagocytic cells, the fluorescent pixel quantification method was used as described []. Graphs depict macrophage and neutrophil numbers. BioImageXD [] was used to obtain the image in . […]


Integrin α2β1 in nonactivated conformation can induce focal adhesion kinase signaling

Sci Rep
PMCID: 5469853
PMID: 28611383
DOI: 10.1038/s41598-017-03640-w

[…] tes, but was mainly located in other plasma membrane areas (Fig. ) in a very similar manner as was seen in the cells plated on EV1 (Fig. ). Based on the quantitative image analyses performed with the BioimageXD software, we detected the colocalization of wild type α2β1 with talin-1, α-actinin and vinculin, whereas α2E336A colocalized with talin-1 and α-actinin, but clearly less with vinculin (Fig. […]


Keratins regulate colonic epithelial cell differentiation through the Notch1 signalling pathway

Cell Death Differ
PMCID: 5442467
PMID: 28475172
DOI: 10.1038/cdd.2017.28
call_split See protocol

[…] oscope with × 63/1.2 water objective was used for image detection (, , , ). Zeiss Zen image software was used for image analysis. Heatmap images () from confocal microscopy data were created with the BioImageXD software. All images in the individual panels were acquired with the same settings and adjusted for brightness and contrast identically using Photoshop CS5 (Adobe, CA, USA).Immunohistochemi […]


T3SS Independent Uptake of the Short Trip Toxin Related Recombinant NleC Effector of Enteropathogenic Escherichia coli Leads to NF κB p65 Cleavage

PMCID: 5390045
PMID: 28451521
DOI: 10.3389/fcimb.2017.00119

[…] once in ddH2O. Cells were visualized using a Zeiss LSM 510, Zeiss LSM 780, or Zeiss LSM 800 confocal laser-scanning microscope. Quantification of co-localization was performed with the free available BioImageXD software (Kankaanpää et al., ). Briefly, LSM files were uploaded to BioImage XD to analyze a pixel-based co-localization between two channels of interest. Thresholds were adjusted automatic […]


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BioImageXD institution(s)
Department of Biochemistry and Food Chemistry, University of Turku, Turku, Finland
BioImageXD funding source(s)
This research was funded by the Academy of Finland (projects 127168 and 114727), the FinNano nanoscience research programme, the Finnish Funding Agency for Technology and Innovation, the Sigrid Juselius Foundation, the National Doctoral Programme in Informational and Structural Biology (ISB), and the European Union 7th framework program (MetaFight).

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