Image Drivers

The slideio module accesses images through a system of image drivers. A driver implements an image format specifics. The driver’s capabilities depend on the image format. The table below contains information about driver capabilities.

Driver

Multiple Scenes

Z Stacks

Time Frames

CZI

yes

yes

yes

SVS

yes

no

no

AFI

yes

no

no

GDAL

no

no

no

CZI driver

Overview

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.

Metadata

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

SVS driver

SVS driver exposes images extracted from Aperion SVS slides. Each Slide objects contains at least one Scene object - image itself. Another Scene objects represent thumbnail, label, and macro.

Scene naming

The following scene names are used:

  • Image: main image;

  • Macro: macro image;

  • Thumbnail: thumbnail image;

  • Label: label image;

Main image is always the first in the scene collection.

Metadata

Slide property raw_metadata returns a string extracted from “Image Description” tiff tag of the main image tag directory.

AFI driver

AFI images is a collection of SVS images boundled together by an xml file with extention “afi”. Each SVS image is represented by a separated Scene object. Slide property raw_metadata always returns an empty string.

GDAL driver

GDAL driver opens generic formats like jpeg, png, tiff, etc. Slide object always contains a single Scene object.

Slide property raw_metadata always returns an empty string.