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

SCN

yes

no

no

GDAL

no

no

no

ZVI

no

yes

no

DCM

yes

yes

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.

Auxiliary images

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

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.

Auxiliary images

The driver supports auxiliary images for Slide objects.

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.

SCN driver

SCN driver allows reading of images produced by a popular Leica SCN400 scanner. Files produced by the scanner have extension .scn and normally contain muliple images such as high resolution scanes of different regions of tissue, thumbnails, lables and barcodes. Each of such internal images exposed as a separated scene objects. Scene property “rect” descripes size of the image and offset of the region.

Scene naming

Names of scenes are taken from an xml metadata document located in the “Image Description” tiff tag.

Metadata

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

Auxiliary images

The driver supports auxiliary images for Slide objects.

GDAL driver

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

Metadata

Slide property raw_metadata always returns an empty string.

ZVI driver

ZVI driver opens images produced by Carl Zeiss AxioVision microscope. The files can containe 2D or 3D images. Slide object always contains a single Scene object.

Metadata

raw_metadata property of a Slide object always returns an empty string.

DCM driver

DCM driver opens DICOM images and directories. The path parameter in open_slide function can be one of the following:

  • path to a DICOM image;

  • path to a DICOMDIR file;

  • path to a difrectory with DICOM files.

Each Scene object of a slide corresponds to a single series for a study and a patient. If path parameter in the open_slide function references a DICOMDIR file or a directory with DICOM files, all images are sorted by series, study and patient and a collection of scene objects is created.

Metadata

raw_metadata property of a Slide object always returns an empty string. raw_metadata property of a Scene object returns json representation of DICOM tags for the first image of the scene.

Auxiliary images

Auxiliary images are not supported by the driver.