You signed in with another tab or window. Reload to refresh your session.You signed out in another tab or window. Reload to refresh your session.You switched accounts on another tab or window. Reload to refresh your session.Dismiss alert
Copy file name to clipboardExpand all lines: _pages/plugins/trackmate/scripting/scripting.md
+17-6Lines changed: 17 additions & 6 deletions
Original file line number
Diff line number
Diff line change
@@ -39,8 +39,9 @@ Here is an example of full tracking process, using the easy image found in the [
39
39
- Then the [TrackMate](/plugins/trackmate) object performs all the steps needed.
40
40
- The final results is displayed as an overlay.
41
41
42
-
{% include code org='fiji' repo='TrackMate' branch='master' path='scripts/ExampleScript_1.py' %}
43
-
42
+
{% include code org='fiji' repo='TrackMate' branch='master' path='scripts/ExampleScript_ExecTracking.py' %}
43
+
44
+
44
45
## Loading and reading from a saved TrackMate XML file
45
46
46
47
Scripting is a good way to interrogate and play non-interactively with tracking results. The example below shows how to load a XML TrackMate file and rebuild a full working model from it.
@@ -49,9 +50,10 @@ That way you could for instance redo a full tracking process by only changing on
49
50
50
51
For the example below to work for you, you will have to edit line 25 and put the actual path to your TrackMate file.
51
52
52
-
{% include code org='fiji' repo='TrackMate' branch='master' path='scripts/ExampleScript_2.py' %}
53
+
{% include code org='fiji' repo='TrackMate' branch='master' path='scripts/ExampleScript_ReadTrackMateFile.py' %}
53
54
54
-
## Export spot, edge and track numerical features after tracking
55
+
56
+
## Display spot, edge and track numerical features after tracking
55
57
56
58
This example shows how to extract numerical features from tracking results.
57
59
@@ -72,7 +74,16 @@ Finally, depending on their type, numerical features are not stored at the same
72
74
73
75
Check the script below to see a working example.
74
76
75
-
{% include code org='fiji' repo='TrackMate' branch='master' path='scripts/ExampleScript_3.py' %}
77
+
{% include code org='fiji' repo='TrackMate' branch='master' path='scripts/ExampleScript_GetTrackingData.py' %}
78
+
79
+
80
+
## Exporting to TrackMate file, to CSV files, to simple track files
81
+
82
+
This script demonstrates several ways by which TrackMate data can be exported to files. Mainly: 1/ to a TrackMate XML file, 2/ & 3/ to CSV files, 4/ to a simplified XML file, for linear tracks.
83
+
84
+
{% include code org='fiji' repo='TrackMate' branch='master' path='scripts/ExampleScript_ExportToFiles.py' %}
85
+
86
+
76
87
77
88
## Manually creating a model
78
89
@@ -104,7 +115,7 @@ Spot quality and link cost are typically useful to quantify automatic spot detec
104
115
105
116
The script below does this: 
106
117
107
-
{% include code org='fiji' repo='TrackMate' branch='master' path='scripts/ExampleScript_4.py' %}
118
+
{% include code org='fiji' repo='TrackMate' branch='master' path='scripts/ExampleScript_CreateTrackingData.py' %}
108
119
109
120
## Making TrackMate macro recordable with a 64-line script
0 commit comments