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Imagedata: A Python library to handle medical image data in NumPy array subclass Series

2022; Open Journals; Volume: 7; Issue: 73 Linguagem: Inglês

10.21105/joss.04133

2475-9066

Erling Andersen,

AI in cancer detection

Imagedata is a python library to read and write medical image data into Series objects.In particular, imagedata will read, sort and write DICOM ® 3D and 4D series based on defined attributes.As far as possible, imagedata will handle geometry information between the medical image data formats like DICOM, NIfTI (Cox et al., 2004) and ITK (Yoo et al., 2002). Imagedata provides a Series class inheriting thenumpy.ndarray class (Harris et al., 2020), adding DICOM data structures.Plugins provide functions to import and export DICOM and other data formats.The DICOM plugin can read complete series, sorting the data as requested into multidimensional arrays.Input and output data can be accessed on various locations, including local files, DICOM servers and XNAT servers (Marcus et al., 2007).The Series class enables NumPy and derived libraries (like SciPy (Virtanen et al., 2020)) to work on medical images, simplifying input and output.A feature is the conversion between different image formats.E.g., a pipeline based on a clinical DICOM series can be converted to NIfTI, processed by some NIfTI-based tool (e.g.FSL (Smith et al., 2004)).Finally, the result can be converted back to DICOM and stored as a new series in PACS (Picture Archive and Communication system).A viewer is included, allowing the display of a stack of images, including modifying window width and centre, and scrolling through 3D and 4D image stacks.A region of interest (ROI) can be drawn, resulting in a mask as a NumPy ndarray, or as an outline.