User Guide

Installation
Tutorial
- Reading data
- Displaying data
- Saving data
- Add DICOM template to other image formats
- Add DICOM template to numpy array
- Sorting DICOM files into multiple Series
Collections
- Introduction
- Reading a Study of Multiple Series
  - Study Attributes
  - GeneralEquipment Attributes
- Reading a Patient with Multiple Study Instances
  - Patient Attributes
  - ClinicalTrialSubject Attributes
- Reading a Cohort of Multiple Patient Instances
  - Cohort Attributes
Viewing Data
- Viewing
  - View multiple series
- Draw region of interest (ROI)
  - Special 4D applications
Jupyter Notebook
- Showing image series
- Drawing a mask
Working with Colors
- Color Data Type
- Creating Color Series
- Saving and Loading Color Series
- Fuse Series and Mask
  - When to blend the original series
Motivation and goals
Design
Series Class
Input/output
- Local files
- ZIP file
- XNAT
- DICOM
Anonymization
Sorting
- Auto-sorting
- User-defined sorting criteria
- N-dimensional sorting
DICOM Attributes
- Series properties
- Full access to DICOM attributes
Segmentation DICOM objects
Non-image DICOM objects
Options
Console Applications
- Included console applications
- Write your own console applications
Examples
- Split MRI diffusion series into separate series for each b value
- Segment an image, display fused image with segmented ROI in red
- Draw a time curve when mask is moved
- Motion correction using FSL MCFLIRT
Plugin Architecture
- Image format plugins
- Archive plugins
- Transport plugins
API Reference
- Series Class
- Collections Class
- Viewer Class
- Imagedata packages
- Formats API Reference
- Archives API Reference
- Transports API Reference
- Apps API Reference
  - Apps Diffusion API Reference