Imaging Applications

XNAT

XNAT is an imaging application used in:

• Clinical Fields such as Radiology, Cardiology, and Oncology

• Research Fields such as Pathology, Neuroscience, Genetics, and Biomedical Engineering

It supports a wide range of imaging modalities, including MRI, CT, PET, and ultrasound

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XNAT Archive

• Identifies files stored in the XNAT Archive, which is the permanent storage location for all XNAT files (e.g., DICOM or project resource files).

• Files here are catalogued in XNAT and tracked in the audit trail. Be mindful of files containing personal health information (PHI) in non-clinical XNAT instances.

XNAT Build

• Reserved path for future use in enhancing the build process. Currently, no files are actively stored or processed here.

XNAT Cache

• Identifies temporary and user-specific files in the XNAT cache directory, including files marked for deletion, which are moved to the cache/DELETED subdirectory.

XNAT Deleted Files

• XNAT doesn’t actually delete data from shared storage, it just moves it and expects users to purge data

• From to the XNAT manual…

When a user or process marks a file for deletion XNAT does not actually delete the file. Instead it is sent to the cache/DELETED directory. It is a good idea to monitor usage of this folder

XNAT Prearchive

• Identifies files stored in the XNAT Prearchive, which serves as an interim storage area where uploaded files can be reviewed for PHI before being moved to the archive.

• Useful for managing ongoing studies and reviewing image sessions before archiving.

XNAT Pipeline

• Reserved path used when installing the XNAT Pipeline Engine. This directory holds files related to pipeline processing

Aperio

Aperio is a platform used by life sciences organizations. Aperio makes scanners and software called Slide Viewer.

• Clinical Fields: Pathology, Oncology, and other diagnostic specialties.

• Research Fields: Histology, Tissue Imaging, and Biomedical Research.

It supports various image formats, including whole slide images and high-resolution microscopy scans.c

Aperio Slide Data

• Aperio uses the extension svs and appears to create one file per slide

• They have been observed to be consistent in size, perhaps around 2GB each
  ss12015_7d34f32e-9dfd-ccbb-8625-1ac22c3d39ad_104201.svs

  ss12015_dd1a154e-f8bd-d495-7333-fddc67d80ae5_132750.svs

Aperio Slide Folders

• Aperio puts slides into date stamped folder such as: /mnt/DigitalPathology/DigitalSlides/Clinical/Aperio/2007-09-25

Aperio DAT Files

• Aperio has been observed creating large amounts of temporary data in a consistent format
  Data0019.dat, Data0020.dat, etc..

Aperio Tile Cache

• Aperio has has been observed creating large amounts of png images in folders called Tile Cache

• We will assume that these are created to enable the application user to view portions of slides with different viewing levels or segments
  2046.2558-516x398@80_0_ims21_viewer.png

  3582.1022-516x516@80_0_ims21_viewer.png

NDP Viewer

NDP Viewer (NDP.view2) is an imaging application used in:

• Clinical Fields such as Pathology and Histology

• Research Fields such as Cellular Biology, Oncology, and Digital Pathology

It designed for high-resolution viewing and analysis of whole-slide images from microscopes such as NDPi files, NDPi (JPEG CR), NDPis and vmu files

Find NDP.view Slides

• NDP Viewer is designed to view slides taken on the Hamamatsu NanoZoomer system

Find NDP.view Log Files

• NDP Viewer can generate very large log files, we have seen files up to 292GB in size