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npy2bdv: writing numpy arrays to Fiji/BigDataViewer HDF5 files

integration_instructionsResearch softwarekeyboard_double_arrow_right Software 04 Aug 2020 English Publisher:ZenodoFunded by:EC | Lightsheetelegans
Authors: Nikita Vladimirov;

doi: 10.5281/zenodo.3971782 , 10.5281/zenodo.3971783 , 10.5281/zenodo.6148906

npy2bdv: writing numpy arrays to Fiji/BigDataViewer HDF5 files

Abstract

Bridging library between Python and HDF5 file format used in Fiji/BigDataViewer/BigStitcher community. Writes image stacks (numpy 3d-arrays) into HDF5 files with rich meta-information saved in an accompanying XML file. Also supports basic reading from HDF5 into numpy arrays. Default options are optimized for high-speed writing in custom microscopes, e.g. streaming images at full camera speed.

Related Organizations
Keywords

Python, HDF5, Fiji, BigDataViewer, BigStitcher, image processing

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selected citations
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This is an alternative to the "Influence" indicator, which also reflects the overall/total impact of an article in the research community at large, based on the underlying citation network (diachronically).
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popularity
This indicator reflects the "current" impact/attention (the "hype") of an article in the research community at large, based on the underlying citation network.
BIP!Popularity provided by BIP!
influence
This indicator reflects the overall/total impact of an article in the research community at large, based on the underlying citation network (diachronically).
BIP!Influence provided by BIP!
impulse
This indicator reflects the initial momentum of an article directly after its publication, based on the underlying citation network.
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