TrackScheme error in TrackMate

Dear Jean-Yves,

We recently came across an error whilst manually correcting tracks with TrackScheme. We tried to re-open a saved XML file using the Load a TrackMate file function and although everything opens regularly at first, we get this error message.

After opening the TrackScheme editor many tracks seem to be lost.

Do you know what could be done about this problem?

Thanks in advance!

Hi @disputator1991
No though it seems like your xml is corrupted: the ‘loop not allowed’ error means that a link links the same spot. You probably want to check that a link doest not have the same spot as source and target.
Best
jy

Dear Jean-Yves,

I am sorry to bother you yet again, but we are continously experiencing problems with editing, saving and re-opening XML files generated with TrackMate. We are currently editing large datasets generated by TrackMate and they all require manual editing of the tracks. Unfortunately one completely edited XML file now can not be re-opened, instead we get the following error in the Log window:

Problem reading the Model:
Unknown spot ID: 9653

Is there any way we can retrieve this edited data and re-open the XML file with TrackMate?

We would be extremely thankful for any help or advice towards solving this problem.

Best regards,

Christian

Hi Christian

Bon, the error is caused when rebuilding the graph: TrackMate look for a spot with ID=9653 and cannot find it.

  • We have to put it manually back by editing the XML file and adding a spot element like this
    < Spot ID=“9653” etc…
    by copy pasting another one. The problem is that we do not know what X, Y, Z and FRAME so it will land at an unexpected place.

  • Another solution is to remove the edges that use it. Check with a text editor if you have a < Edge SPOT_SOURCE_ID=“3757” SPOT_TARGET_ID="5154"
    that use the incriminated ID. Removing them might solve the problem but maybe disconnect a track.

Of course, make copies before that.

If nothing works, send me the file and be patient.
Courage!
jy

2 Likes

Hi Jean-Yves,

thanks for the help. We removed the erroneous Spot ID in the XML file and the edited Tracks could be re-opened normally again.

Many thanks!!!

1 Like

Dear Jean-Yves @tinevez,

I am running across the same problem as mentioned in this thread. While trying to load a file I get the following message:

Problem reading the model:
Unknown spot ID: 4

I tried both adding a spot with ID 4 (same message) and removing the edges using this ID. It did not work, when I remove the edges the same message appears with another spot ID. When I remove the edges of 4 the new unknown spot ID is 60, when I removed 60 the new unknown spot ID is 27, see the extract of the file here:


<AllTracks>
      <Track name="Track_0" TRACK_ID="0" NUMBER_SPOTS="4" NUMBER_GAPS="0" LONGEST_GAP="0" NUMBER_SPLITS="1" NUMBER_MERGES="0" NUMBER_COMPLEX="0" TRACK_INDEX="0" TRACK_X_LOCATION="785.7753189284406" TRACK_Y_LOCATION="184.46191914814696" TRACK_Z_LOCATION="0.0" TRACK_MEAN_SPEED="NaN" TRACK_MAX_SPEED="NaN" TRACK_MIN_SPEED="NaN" TRACK_MEDIAN_SPEED="NaN" TRACK_STD_SPEED="NaN" TRACK_MEAN_QUALITY="-1.0" TRACK_MAX_QUALITY="-1.0" TRACK_MIN_QUALITY="-1.0" TRACK_MEDIAN_QUALITY="-1.0" TRACK_STD_QUALITY="0.0">
        <Edge SPOT_SOURCE_ID="4" SPOT_TARGET_ID="7" LINK_COST="-1.0" EDGE_TIME="-Infinity" EDGE_X_LOCATION="792.4830250792822" EDGE_Y_LOCATION="182.73089820599427" EDGE_Z_LOCATION="0.0" VELOCITY="NaN" DISPLACEMENT="16.1690699505085" />
        <Edge SPOT_SOURCE_ID="4" SPOT_TARGET_ID="11" LINK_COST="-1.0" EDGE_TIME="-Infinity" EDGE_X_LOCATION="778.2021023065225" EDGE_Y_LOCATION="187.058450561376" EDGE_Z_LOCATION="0.0" VELOCITY="NaN" DISPLACEMENT="13.684922136632801" />
        <Edge SPOT_SOURCE_ID="1" SPOT_TARGET_ID="4" LINK_COST="-1.0" EDGE_TIME="-Infinity" EDGE_X_LOCATION="785.5589413106716" EDGE_Y_LOCATION="184.0291639126088" EDGE_Z_LOCATION="0.0" VELOCITY="NaN" DISPLACEMENT="2.448033293144256" />
      </Track>
      <Track name="Track_1" TRACK_ID="1" NUMBER_SPOTS="21" NUMBER_GAPS="0" LONGEST_GAP="0" NUMBER_SPLITS="1" NUMBER_MERGES="0" NUMBER_COMPLEX="0" TRACK_INDEX="1" TRACK_X_LOCATION="539.2593901129446" TRACK_Y_LOCATION="422.4154765176375" TRACK_Z_LOCATION="0.0" TRACK_MEAN_SPEED="NaN" TRACK_MAX_SPEED="NaN" TRACK_MIN_SPEED="NaN" TRACK_MEDIAN_SPEED="NaN" TRACK_STD_SPEED="NaN" TRACK_MEAN_QUALITY="-1.0" TRACK_MAX_QUALITY="-1.0" TRACK_MIN_QUALITY="-1.0" TRACK_MEDIAN_QUALITY="-1.0" TRACK_STD_QUALITY="0.0">
        <Edge SPOT_SOURCE_ID="60" SPOT_TARGET_ID="63" LINK_COST="-1.0" EDGE_TIME="-Infinity" EDGE_X_LOCATION="540.1867227605265" EDGE_Y_LOCATION="423.7755644007575" EDGE_Z_LOCATION="0.0" VELOCITY="NaN" DISPLACEMENT="1.9353402485645739" />
        <Edge SPOT_SOURCE_ID="57" SPOT_TARGET_ID="60" LINK_COST="-1.0" EDGE_TIME="-Infinity" EDGE_X_LOCATION="540.6194779960647" EDGE_Y_LOCATION="424.6410748718339" EDGE_Z_LOCATION="0.0" VELOCITY="NaN" DISPLACEMENT="0.0" />
        <Edge SPOT_SOURCE_ID="27" SPOT_TARGET_ID="30" LINK_COST="-1.0" EDGE_TIME="-Infinity" EDGE_X_LOCATION="536.291925640683" EDGE_Y_LOCATION="420.31352251645217" EDGE_Z_LOCATION="0.0" VELOCITY="NaN" DISPLACEMENT="13.519705752435755" />
        <Edge SPOT_SOURCE_ID="42" SPOT_TARGET_ID="45" LINK_COST="-1.0" EDGE_TIME="-Infinity" EDGE_X_LOCATION="540.6194779960647" EDGE_Y_LOCATION="424.6410748718339" EDGE_Z_LOCATION="0.0" VELOCITY="NaN" DISPLACEMENT="0.0" />
        <Edge SPOT_SOURCE_ID="21" SPOT_TARGET_ID="24" LINK_COST="-1.0" EDGE_TIME="-Infinity" EDGE_X_LOCATION="533.6953942274539" EDGE_Y_LOCATION="417.7169911032231" EDGE_Z_LOCATION="0.0" VELOCITY="NaN" DISPLACEMENT="10.529389326088014" />
        <Edge SPOT_SOURCE_ID="48" SPOT_TARGET_ID="51" LINK_COST="-1.0" EDGE_TIME="-Infinity" EDGE_X_LOCATION="540.6194779960647" EDGE_Y_LOCATION="424.6410748718339" EDGE_Z_LOCATION="0.0" VELOCITY="NaN" DISPLACEMENT="0.0" />

Any help on this would be greatly appreciated.
Merci!

Ella