Tile Source Conventions

CATMAID does not serve image data itself. Instead, it stores a few critical pieces of information about the image volume and specifies a set of conventions for retrieving image data from a separate image volume host. These conventions are tile source types, which define parameters and URL formats both the CATMAID backend and frontend can use to access image data for rendering and analysis.

This document provides information on the type source types specified by CATMAID, the parameters which they use to retrieve image data, how this is stored in the CATMAID backend, and how to create a new tile source type in the CATMAID backend and frontend.

Tile Source Parameters

Each tile source type uses a subset of the following parameters to determine its source regardless of the specific tiles being retrieved. Though specific APIs may use different names for these parameters, the names provided here are used for consistency in defining tile source types below:

sourceBaseURL (string)
This defines a base URL for the source server and volume, including trailing slash.
dimension (integer array [x, y, z])
Dimension of the image volume in pixels at its original scale level.
resolution (double array [x, y, z])
Resolution of the image volume in nanometers at its original scale level.
numZoomLevels (integer)
The number of zoom levels (downsampling octaves) which the source supports.
fileExtension (string)
Filename extension for image tiles served by the source.

tileWidth (integer)

tileHeight (integer)
Dimensions of image tiles in pixels. For pre-tiled sources, this should be the dimensions of the source tiles, while for dynamic sources this should be the preferred dimension for retrieval and rendering.
orientation (integer|string)

Orientation of the stack relation to project space. Semantically this value is either “XY”, “XZ”, “ZY”, but is usually passed as an integer in {0, 1, 2} enumerating these, respectively.

Currently only DVID tile source types (6, 8) must know orientation directly. Other tile source types encode orientation in the sourceBaseURL.

tileSourceType (integer)
A integer enumerating the types of tile sources listed below.

Tile Parameters

Tile sources may additionally make use of a subset of the following parameters when determining how to retrieve specific tile requests:

row (integer)
The row of the tile in the image grid for this z-slice, e.g., the floor of the tile y origin divided by tileHeight.
col (integer)
The column of the tile in the image grid for this z-slice, e.g., the floor of the tile x origin divided by tileWidth.
zoomLevel (integer)
The zoom level of tiles to retrieve. Zoom level 0 is the original scale, zoom level 1 is the first downsampled octave, etc.
pixelPosition (integer array [x, y, z])
The stack space position in pixels of a location in the plane of the tile. Usually this position is shared for many tile requests, e.g., the center of a stack viewer, and is used only to generate a path using the z location in the stack.

Tile Source Types

Tile source types are listed by the enumeration integer ID referenced by tileSourceType:

1. File-based image stack

URL format:

<sourceBaseUrl><pixelPosition.z>/<row>_<col>_<zoomLevel>.<fileExtension>

2. Request query-based image stack

URL format:

<sourceBaseURL>?x=<col * tileWidth>
               &y=<row * tileHeight>
               &z=<pixelPosition.z>
               &width=<tileWidth>
               &height=<tileHeight>
               &scale=<2^-zoomLevel>
               &row=y
               &col=x

3. HDF5 via CATMAID backend

Note

To use this tile source, the h5py Python library has to be installed.

This is the only tile source type which the CATMAID backend serves directly. Django retrieves tile requests from an image volume stored in an HDF5 file. This is a convenience source intended for quick exploration of small volumes only and does not scale to large volumes or many users.

As an exceptional source, this uses the following tile source parameters that should not be used by any other source:

catmaidURL (string)
Base URL of the CATMAID instance serving the volume, including trailing slash.
projectId (integer)
ID of the CATMAID project.
stackId (integer)
ID of the CATMAID stack.

URL format:

<catmaidURL><projectId>/stack/<stackID>/tile?x=<col * tileWidth>
                                            &y=<row * tileHeight>
                                            &z=<pixelPosition.z>
                                            &width=<tileWidth>
                                            &height=<tileHeight>
                                            &scale=<2^-zoomLevel>
                                            &row=y
                                            &col=x
                                            &file_extension=<fileExtension>
                                            &basename=<sourceBaseURL>
                                            &type=all

4. File-based image stack with zoom level directories

A variation on tile source type 1 where the zoom level is also a directory.

URL format:

<sourceBaseUrl><pixelPosition.z>/<zoomLevel>/<row>_<col>.<fileExtension>

5. Directory-based image stack

Like tile source types 1 and 4, but with all components being directories.

URL format:

<sourceBaseUrl><zoomLevel>/<pixelPosition.z>/<row>/<col>.<fileExtension>

6. DVID imageblk voxels

This type supports loading tiles from voxel data instances in DVID using imageblk (uint8blk, rgba8blk) datatypes.

For DVID imageblk tile sources, sourceBaseURL should reference the data instance REST resource with orientation information directly, that is:

<api URL>/node/<UUID>/<data name>/raw/<dims>/

fileExtension may also specify a quality parameter, e.g., jpg:80.

Because orientations are just permutations of coordinates in the voxel volume, each orientation has a slightly different URL format.

XY format:

<sourceBaseUrl><tileWidth>_<tileHeight>/<col * tileWidth>_<row * tileHeight>_<pixelPosition.z>/<fileExtension>

XZ format:

<sourceBaseUrl><tileWidth>_<tileHeight>/<col * tileWidth>_<pixelPosition.z>_<row * tileHeight>/<fileExtension>

ZY format (actually YZ, see note):

<sourceBaseUrl><tileWidth>_<tileHeight>/<pixelPosition.z>_<row * tileHeight>_<col * tileWidth>/<fileExtension>

Note

Because DVID prefers YZ axis ordering over ZY, note that tiles for that orientation must be transposed to be consistent with other tile source types.

7. Render service

This tile source type retrieves image tiles from the dynamic render service used by the FlyTEM project at Janelia Research Campus.

URL format:

<sourceBaseURL>largeDataTileSource/<tileWidth>/<tileHeight>/<zoomLevel>/<pixelPosition.z>/<row>/<col>.<fileExtension>

8. DVID imagetile tiles

This type supports loading tiles from tile data instances in DVID using imagetile datatypes.

For DVID imagetile tile sources, sourceBaseURL should reference the data instance REST resource directly, that is:

<api URL>/node/<UUID>/<data name>/tile/

Because orientations are just permutations of coordinates in the voxel volume, each orientation has a slightly different URL format.

XY format:

<sourceBaseUrl>xy/<zoomLevel>/<col>_<row>_<pixelPosition.z>

XZ format:

<sourceBaseUrl>xz/<zoomLevel>/<col>_<pixelPosition.z>_<row>

ZY format (actually YZ, see note):

<sourceBaseUrl>yz/<zoomLevel>/<pixelPosition.z>_<row>_col

Note

Because DVID prefers YZ axis ordering over ZY, note that tiles for that orientation must be transposed to be consistent with other tile source types.

9. FlixServer tiles

This type supports loading tiles from a FlixServer instance. This tile server generates images dynamically and supports CATMAID’s default tile source URL format:

<sourceBaseUrl><pixelPosition.z>/<row>_<col>_<zoomLevel>.<fileExtension>

Additional GET parameters can be used to adjust color, dynamic range and gamma mapping:

color = (red,green|blue|cyan|magenta|yellow|white) for coloring
min/max = [0, 2^16] for specifying the dynamic range
gamma = [0, 2^16] for the exponent of a non-linear mapping

For multi-channel images, a comma separated list can be used as parameter value (e.g. color=cyan,magenta).

Backend Representation

Tile source parameters are stored in the Stack Django model. To create a new tile source type, one needs only to establish a convention for the integer that enumerates that type (after communication with the developers) and begin using it in stacks.

To support cropping, the backend also implements tile sources. To support cropping for a new tile source type, implement a method in catmaid.control.cropping.CropJob like other get_tile_path_<tileSourceType> methods that returns the correct URL, then make sure it is called from the CropJob.initialize method.

Frontend Retrieval

The front end implements tile source URL generation in django/applications/catmaid/static/js/tile-source.js. To define a new tile source type, follow the convention of the existing tiles sources by creating a function that returns an object with the appropriate getTileURL, getOverviewURL, and getOverviewLayer methods. The overview URL should locate a thumbnail of the current stack z-section. Then map the tileSourceType enumeration of your tile source type to your implementation in CATMAID.getTileSource.