CZI Image Driver


A CZI image is a collection of multi-dimensional pixel regions (sub-blocks) that are aquired with different parameters. As of version 1.2.2 the following parameters (dimensions) are supported:

  • Channel (C) - index of a channel in a multi-channel data set
  • Slice index (Z) - index of a slice in Z direction.
  • Time point (T) - index of a time frame in a sequentially acquired series of data.
  • Rotation (R) – used in acquisition modes where the data is recorded from various angles.
  • Region (S) – for clustering items in X/Y direction (data belonging to contiguous regions of interests in a mosaic image).
  • Illumination (I) - illumination direction index (e.g. from left=0, from right=1).
  • Acquisition (B) Block index in segmented experiments.
  • Mosaic tile index (I) – this index uniquely identifies all tiles in a specific plane.
  • Phase index (H) – for specific acquisition methods.
  • View index (V) - for multi – view images, e.g. SPIM.

Slideio combines the sub-blocks in 2D-4D(depending if Z slices and time-frames are present) continuous scenes. Each scene corresponds to different sequence of dimensions:

  • Rotation (R).
  • Region (S).
  • Illumination (I).
  • Acquisition (B).
  • Mosaic tile index (I).
  • Phase index (H).
  • View index (V).

Scene naming

The actual values of the dimension parameters are coded in the scene name. For example, scene with name: “s:1 i:0 v:2 h:1 r:0 b:1” corresponds to a region with index 1, illumination index 0, view index 2, phase index 1, rotation angle index 0 and block index 1.


Slide property raw_metadata returns a textual representation of embedded in the slide xml document with image metadata.

Auxiliary images

The driver supports auxiliary images for Slide and Scene objects. Images are extracted from corresponded “attachment” sections of the file.