LoG Detector filter setting used, even though spot manual annotation selected

[wolfgangkeil]

Dear TrackMate Team,

We are using the Trackmate Plugin for several things, some of which allow for automated spot detection and some require manual annotation (not on the same files).

Recently, we've been encountering an issue during manual annotation. After finishing the annotation, and clicking next, all dots disappeared on the image viewer (even though no filters are added). When we continued clicking towards the tracking, it became evident that spots were, in fact, filtered as if going through automated detection!

The output of the LogWindow on a test file were we just annotated 3 spots manually reads something like the one below.
Funny enough, if we go into LoG detection and change the threshold value in the initial thresholding window after spot detection and then go back to manual annotation and start over, it uses the threshold value we had chosen during the LoG detection as if this is somehow kept in memory.

Not sure this is related, but at the same as the above issue arose, we also lost the ability to ADD spots to our manual annotations. Once we click "Next" and then click "<---" to go back, all spots disappear, even after we saved an .xml. This wasn't the case before. Going back normally allowed us to add further spots.

Thanks for looking into this.
Wolfgang

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Image region of interest:
Image data:
For the image named: pos_0_chop_1_trackID_0021.tif.
Matching file pos_0_chop_1_trackID_0021.tif in folder:
Geometry:
X = 0 - 36, dx = 1.00000
Y = 0 - 36, dy = 1.00000
Z = 0 - 14, dz = 2.72730
T = 0 - 29, dt = 1.00000
Initial thresholding with a quality threshold above -246.6 ...
Starting initial filtering process.
Retained 0 spots out of 0.

Calculating spot features...
Calculating features done in 0.0 s.

Performing spot filtering on the following features:
No feature threshold set, kept the 0 spots.
Initial thresholding with a quality threshold above -246.6 ...
Starting initial filtering process.
Retained 3 spots out of 3.

Calculating spot features...
Calculating features done in 0.0 s.

Performing spot filtering on the following features:
No feature threshold set, kept the 3 spots.

Configured tracker LAP Tracker with settings:

• max frame gap: 5
• alternative linking cost factor: 1.05
• linking feature penalties:
• linking max distance: 20.0
• gap closing max distance: 20.0
• merging feature penalties:
• splitting max distance: 15.0
• blocking value: Infinity
• allow gap closing: true
• allow track splitting: false
• allow track merging: false
• merging max distance: 15.0
• splitting feature penalties:
• cutoff percentile: 0.9
• gap closing feature penalties:

Starting tracking process.
Tracking done in 0.0 s.
Found 1 tracks.

• avg size: 3.0 spots.
• min size: 3 spots.
• max size: 3 spots.

---

[tinevez]

Hello @wolfgangkeil
I am revisiting this issue. Just to be sure: Do you start manual annotations by using the Manual tracking with TrackMate plugin?