ImageDS-Experiments

Public DICOM toolkits

DCMTK - Github

Dicom Toolkit - DCMTK

GDCM

Used by the Insight Toolkit...

Using Insight TookKit - ITK

Docker Install of ITK

Example

• docker build -t try_itk:centos7 . # For building
• docker run -it try_itk:centos7 # For a bash shell in the docker image

Documentation of ITK

ITK Usage with ImageDS

• First experiment to read from a DICOM image and write to ImageDS and vice versa. Start with
  • Implement itk's readers and writers
    • itk::ImageFileReader
    • itk::ImageFileWriter
  • Figure out ImageDS for the images
    • One image per tiledb/array versus all images in one array.
    • How do we use itk? Do we read in the DICOM image, filter, register and segment before storing in ImageDS?
    • Can all the images be registered/segmented/scaled in a similar fashion?
    • If using Hadoop FileSystem HDFS, filesize is not a problem and we can store all the images together. Also, using tiledb we can write out one image/sets of images at a time, concurrently as each will write to a different fragment and consolidate if necessary later.

To read...

Comparison of using png/LMDB/HDF5 for storing images using python

Paper - Implementation of an image storage system using HDF5 as front end and tiledb as storage