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Convention for Stack Image Sources
This is legacy documentation. For current documentation see tile source conventions on catmaid.org.
This document describes the ongoing, proof-of-concept to use arbitary TileServers other than the pre-specified tile server in CATMAID. A proof-of-concept implementation using Ilastik (with Volumina & LazyFlow) is in development here.
Authors: Bernhard Kausler, Stephan Gerhard
Default URL: /metadata
To be implemented as a Django-view that depending on the tile_source_type, fetches from the CATMAID database stack metadata, or from the TileServer
title the stack title
comment general comments about the stack, like provenance
dimension (x,y,z)
resolution (x,y,z)
tilesource_url default: /
labelupload_url default: /labelupload
file_extension default: png
tile_width default: 256
tile_height default: 256
min_zoom_level default: -1 (do we need this?)
Default URL: /
x x location in what volumina calls physical coordinates, i.e. the second axis axis of a (t,x,y,z,c) dataset
y y location in what volumina calls physical coordinates, i.e. the third axis axis of a (t,x,y,z,c) dataset
z z location in what volumina calls physical coordinates, i.e. the forth axis axis of a (t,x,y,z,c) dataset
width the tile width, should match the metadata tile_width
height the tile height, should match the metadata tile_height
scale a float scale factor, defined as 1/2**zoomlevel
row e.g. set to 'y' to mean that the row axis (from top-left to bottom-left) uses the third axis of the dataset
col e.g. set to 'x' to mean that the column axis (from top-left to top-right) uses the forth axis of the dataset
Default URL: /labelupload
The labeled pixels (RGBA) within a field-of-view need to be uploaded to the TileServer and integrated in the appropriate data store (e.g. HDF5 dataset for labels) or used for prediction. The definition of the field-of-view is similar to the definition of the tiles. It basically defines a shape and position that can be used to index into HDF5 datasets.
x x location in what volumina calls physical coordinates, i.e. the second axis axis of a (t,x,y,z,c) dataset
y y location in what volumina calls physical coordinates, i.e. the third axis axis of a (t,x,y,z,c) dataset
z z location in what volumina calls physical coordinates, i.e. the forth axis axis of a (t,x,y,z,c) dataset
row e.g. set to 'y' to mean that the row axis (from top-left to bottom-left) uses the third axis of the dataset
col e.g. set to 'x' to mean that the column axis (from top-left to top-right) uses the forth axis of the dataset
image the pixel data encoded as RGBA-based PNG
metadata metadata about particular labels as a list
{
"name": "eraser",
"color": 'rgba(255,255,255,1.0)',
"id": 0
},
{
"name": "cell membrane",
"color": 'rgb(255,0,0)',
"id": 1
},
{
"name": "cell interior",
"color": 'rgb(0,255,0)',
"id": 2
},
{
"name": "mitochondria",
"color": 'rgb(0,0,255)',
"id": 3
}