index.md

layout	title
page	Specification

Definition

This is an example of a track specification:

• Object: an object of interest (such as a cell) detected in a microscopy image
• Link: a linear, temporal collection of objects
• Track: a collection of links

Scenarios

A simple track

The following shows an input consisting of 3 images.

The case illustrated shows 3 objects identified in each frame. At this stage, there is no association between objects across the frames.

{:class="img-responsive"}

The objects table is:

Object_ID	Frame	X	Y
1	1
2	1
3	1
4	2
5	2
6	2
7	3
8	3
9	3

With a linking algorithm, an association is created between objects across frames, and links are produced. The colored lines in the next figure represent these links.

{:class="img-responsive"}

The links table is:

Link_ID	Object_ID
1	1
1	4
1	7
2	2
2	5
2	8
3	3
3	6
3	9

In this table, the foreign key to the objects table is the Object_ID. This specification requires unique Object_ID in the objects table. If this is not the case, an extra frame column MUST be present in the links table.

Finally, tracks are derived from objects + links information: {:class="img-responsive"}

In this simple case, the tracks table would look like this:

Track_ID	Link_ID
1	1
2	2
3	3

Gap-closing

A gap event occurs when an object of interest (a cell) disappears for one or more frames, then reappears.

This case can be illustrated as follows:

{:class="img-responsive"}

The detected object is lost at frame 3, and then reappears at frame 4.

The objects table is:

Object_ID	Frame	X	Y
1	1
2	2
3	4
4	5

In this specification, the gap-closing event is explicitly represented in the repetition of the Object_ID reference. Therefore, the links table can take one of the three following forms:

• A

Link_ID	Object_ID
1	1
1	2
1	3
2	3
2	4

Here, the Object_ID repeated is the one after the gap event, and the tracks table is:

Track_ID	Link_ID
1	1
1	2

This case can be illustrated as follows:

{:class="img-responsive"}

• B

Link_ID	Object_ID
1	1
1	2
2	2
2	3
2	4

Here, the Object_ID repeated is the one before the gap event, and the tracks table is:

Track_ID	Link_ID
1	1
1	2

This case can be illustrated as follows:

{:class="img-responsive"}

• C

Link_ID	Object_ID
1	1
1	2
2	3
2	4
3	2
3	3

Here, both the Object_ID reference of the objects before and after the event are repeated, and the corresponding tracks table is:

Track_ID	Link_ID
1	1
1	2
1	3

This case can be illustrated as follows:

{:class="img-responsive"}

Split/merge events

• Split event: when a detected object seems to divide in two objects in the next frame.
• Merge event: when two detected objects seem to collide into one object.

A split event

A split event looks like this:

{:class="img-responsive"}

The objects table in this case is:

Object_ID	Frame	X	Y
1	1
2	2
3	3
4	3
5	4
6	4
7	5
8	5

The links table is:

Link_ID	Object_ID
1	1
1	2
1	3
1	5
1	7
2	2
2	4
2	6
2	8

In this case, the split event is encoded in the repetition of the Object_ID reference: Object_ID = 2 in Link_ID = 1 and Link_ID = 2 (1:n relationship from objects to links).

The corresponding tracks table is:

Track_ID	Link_ID
1	1
1	2

Links 1 and 2 are assigned to the same track, track 1.

A merge event

A merge event looks like this:

{:class="img-responsive"}

The objects table in this case is:

Object_ID	Frame	X	Y
1	1
2	1
3	2
4	2
5	3
6	4
7	5

The links table is:

Link_ID	Object_ID
1	1
1	3
1	5
2	2
2	4
2	5
2	6
2	7

Again, the merge event is encoded in the repetition of the Object_ID reference: Object_ID = 5 in Link_ID = 1 and Link_ID = 2 (1:n relationship from objects to links).

The corresponding tracks table is:

Track_ID	Link_ID
1	1
1	2

Links 1 and 2 are assigned to the same track, track 1.

Combination of events

A split event with a gap-closing

A split event in combination with a gap-closing event looks like this: {:class="img-responsive"}

The objects table in this case is:

Object_ID	Frame	X	Y
1	1
2	2
4	3
5	4
6	4
7	5
8	5

The links table can take one of the following forms:

• A

Link_ID	Object_ID
1	1
1	2
1	5
3	5
3	7
2	2
2	4
2	6
2	8

{:class="img-responsive"}

The corresponding tracks table is:

Track_ID	Link_ID
1	1
1	2
1	3

• B

Link_ID	Object_ID
1	1
1	2
3	2
3	5
3	7
2	2
2	4
2	6
2	8

{:class="img-responsive"}

The corresponding tracks table is:

Track_ID	Link_ID
1	1
1	2
1	3

• C

Link_ID	Object_ID
1	1
1	2
3	2
3	5
2	5
2	7
4	2
4	4
4	6
4	8

{:class="img-responsive"}

The corresponding tracks table is:

Track_ID	Link_ID
1	1
1	2
1	3
1	4

File formats

See this repository for more information about a Data Package-based file format which supports this specification.

Requirements

The objects table and the links table MUST be part of this specification. The tracks table can be inferred from the first two, and it can therefore MAY be part of the specification.