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SCIFIO / SCientific Image Format Input and Output

A library software to create extensible framework for the reading, writing, and translation of images. SCIFIO was designed to provide the architecture that will equally facilitate: i) the conversion of additional formats into supported open-exchange formats such as OME-TIFF and ii) the integration of additional scientific open-exchange formats. The extensible design of SCIFIO facilitates community contribution, the establishment of domain-specific metadata standards, and integration into a unified system capable of adapting to the demands of scientific imaging analysis.

OME Files

Converts the metadata in proprietary scientific image file formats into the open Open Microscopy Environment (OME) Data Model. OME Files provides a seamless, performant way for these calculations to use OMETIFF. It provides interoperability with the wide range of existing software supporting OME-XML and OME-TIFF formats. The tool is several-fold faster reading and writing metadata from a multi-dimensional fluorescence image. It is a performant, useful resource for reading and writing OME-TIFF in several different use cases.


Permits to convert proprietary Philips PAR/REC images to neuroimaging informatics technology initiative (NIfTI). dcm2niix is easy to use, offers features to specify output file names. It is suitable for clinical environments. The tool is able to convert diffusion vectors and shows good results for job with Computerized-Tomography (CT) scans. It offers a graphical user interface (GUI) that permits to display an example for how user files will appear. dcm2niix offers a way to save the output to a specific folder or whether the NIfTI images should be created in the same folder as the input DICOM files.