Deep Link URL Format¶
CATMAID supports deep link URLs that allow users to share persistent references to particular stack locations and views. These URLs also support opening tools, multiple stack viewers, and limited specialized behaviors such as activating nodes in the tracing tool. Which stack mirror is used for a referenced stack is up to the client instance.
CATMAID deep link URLs are standard HTTP URLs with query strings, for example:
https://localhost/cat/?pid=1&zp=0&yp=0&xp=0&tool=navigator
All URLs begin with the protocol, hostname and path (including trailing slash) of the CATMAID instance configured during installation.
Required Query Parameters¶
pid
(integer)ID of the project to open.
zp
(integer)
yp
(integer)
xp
(integer)Coordinates in project space (nm) to center in the stack viewer.
tool
(string)Name of the tool to open. Must be one of
navigator
,tracingtool
, orclassification_editor
.
Optional Query Parameters¶
active_node_id
(integer)Specifies the ID of a node to activate in the tracing tool.
sid<n>
(integer)Opens the stack with this ID in a stack viewer. Multiple stacks can be opened by passing incremental indexes, i.e.,
sid0
,sid1
, etc. The index must start at 0.s<n>
(integer)Zoom level for the corresponding stack ID above. That is,
s0
specifies the initial zoom level for the stack viewer viewing the stack ID passed insid0
.composite
(integer)If
1
, load all stacks as layers in a single stack viewer rather than separate stack viewers.sg
(integer)Open a stack group. If present, individual stacks are ignored.
sgs
(integer)Initial zoom level for a loaded stack group.
current_dataview
(integer)ID of a data view to switch to.
layout
(string)An optional layout specification in the format of layouts described in the Settings Widget. E.g.
layout=h(XY, { type: "neuron-search", id: "neuron-search-1"}, 0.6)
to show a Neuron Search widget in a 1/3 wide column on the right. Depending on the widget referenced, additional options are available. For instance, the Neuron Search can be instructed to search for a particular annotation right away:layout=h(XY, { type: "neuron-search", id: "neuron-search-1", options: {"annotation-name": "papers"}}, 0.6)
. Available options are collected below. Additionally, individual layout elements can have a"skeletons"
parameter (like the"options"
parameter), which can take a list of skeleton IDs or, alternatively objects having anid
and acolor
field. The color can be defined in terms of common CSS color representations like “red” or “rgb(0.2,1,0.5)”. These skeletons are added to the newly created widgets, if possible.token
(string)An optional project token to give access to a particular project. If this is used, the link becomes essentially an invitation link. With admin permissions, this tokens can be generated in the Project Management widget.
Legacy Query Parameters¶
These parameters may be found in old URLs but are no longer generated and may not be properly processed.
x
(integer)
y
(integer)
z
(integer)Coordinates in project space to center the stack viewer. Used in an obsolete query format where no project or stack ID were specified and defaulted to
1
.s
(integer)Zoom level for the stack viewer.
active_skeleton_id
(integer)Specifies the ID of a skeleton to activate in the tracing tool.
account
(string)Username with which to login to CATMAID.
password
(string)Password with which to login to CATMAID.
URL widget options¶
Neuron Search
Supports
annotation-name
to search for a particular annotation andwith-subannotations
to include sub-annotations for this search.