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BioImageXD specifications

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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

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Publication for BioImageXD

BioImageXD in publications

 (38)
PMCID: 5795705
PMID: 29410779
DOI: 10.1080/20013078.2017.1422675

[…] was implemented to improve 3d co-localization analysis of nuclear dapi staining and exosome cellvue staining., voxel-based co-localization analysis of dapi and cellvue signals was performed using bioimagexd software []. automatic threshold calculation was not suitable for sparse cellvue signals, constant manual thresholds were set for all analysed time points and samples, and 10 costes […]

PMCID: 5929907
PMID: 29712618
DOI: 10.7554/eLife.32490.032

[…] scores were discussed and consensus scores were determined., for quantification of the assay in 3d-fibrin gels, confocal stacks where analysed with the open source software bioimage xd (http://www.bioimagexd.net/) () using the 'skeleton' tool in the 3d modules of the software. cell clusters were identified by thresholding the intensity of melanoma gfp fluorescence. the skeleton function […]

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

[…] 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, […]

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

[…] 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 ., statistical analysis was performed using prism 6 (graphpad). survival assays are represented in kaplan-meier graphs and analysed with a log rank […]

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

[…] 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 […]


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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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