Weird, anomalous track links with FIJI TrackMate-Trackastra plugin

[gopher-confocal]

I'm repeatedly getting weird, anomalous tracks with the FIJI TrackMate-Trackastra plugin. Sometimes I get extended track links between cells that aren't near each other.

Hopefully, you can see the image. Has anyone else reported this? How do I resolve these weird track links? I have example XML files and TIFF data in this Google Drive folder. I would appreciate greatly if someone would take a look at my data and XML files and let me know what's going wrong. Thank you for your help!

[bentaculum]

Hi @gopher-confocal, thanks for reporting this. I have seen these long links once in a while when input segmentations are a bit off, and as a result trackastra somewhat desperately tries to find links to continue tracks. As a simple fix, can you try setting the max_distance slider to a lower threshold?

[gopher-confocal]

How do I do that in the FIJI TrackMate plugin? I don't see a window option for adjusting any Trackastra parameters. <img width="336" height="577" alt="Image" src="https://github.com/user-attachments/assets/84642825-8ca6-43d1-966c-89f9a50ce5c8" /> How do I run Trackastra 0.5.5 in FIJI TrackMate? Thank you for your help. *UIC Image Analysis Office Hours:* Mondays 9 - 10:30 AM, Jackson Hall, rm. 1-153 Mondays 2 - 3:30 PM, Snyder Hall, rm. 23 Fridays 9 - 10:30 AM, CCRB, rm. 1-220 **Any work utilizing UIC equipment or staff support must acknowledge the University Imaging Centers in publications and presentations. SCR 020997**

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________________________________________________ Mary E. Brown, Pharm.D. Imaging Specialist/Research Professional 3/Lead Image Data Analyst University Imaging Centers Snyder Hall, rm. 23F 1475 Gortner Avenue Saint Paul, MN 55108 Email: ***@***.*** Phone: 773-458-3090

On Fri, Aug 7, 2026 at 8:36 AM Benjamin Gallusser ***@***.***> wrote: *bentaculum* left a comment (weigertlab/trackastra#69) <#69 (comment)> Hi @gopher-confocal <https://github.com/gopher-confocal>, thanks for reporting this. I have seen these long links once in a while when input segmentations are a bit off, and as a result trackastra somewhat desperately tries to find links to continue tracks. As a simple fix, can you try setting the max_distance slider to a lower threshold? — Reply to this email directly, view it on GitHub <#69?email_source=notifications&email_token=AMB72WAUZAQXLK6ARTHB6HD5IXLNFA5CNFSNUABFM5UWIORPF5TWS5BNNB2WEL2JONZXKZKDN5WW2ZLOOQXTKMRRG43TGOJZHA32M4TFMFZW63VHNVSW45DJN5XKKZLWMVXHJLDGN5XXIZLSL5RWY2LDNM#issuecomment-5217739987>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AMB72WGJH2A7LNTXAALKKZ35IXLNFAVCNFSNUABFKJSXA33TNF2G64TZHM3TMOJRGQ3DMMBXHNEXG43VMU5TKMBWGEYTSMZVGQ3KC5QC> . Triage notifications, keep track of coding agent tasks and review pull requests on the go with GitHub Mobile for iOS <https://github.com/notifications/mobile/ios/AMB72WEUOIV23OSBVJDFWUD5IXLNFA5CNFSNUABFM5UWIORPF5TWS5BNNB2WEL2JONZXKZKDN5WW2ZLOOQXTKMRRG43TGOJZHA32M4TFMFZW63VHNVSW45DJN5XKKZLWMVXHJKTGN5XXIZLSL5UW64Y> and Android <https://github.com/notifications/mobile/android/AMB72WCEU4FWBMW7R37ONSD5IXLNFA5CNFSNUABFM5UWIORPF5TWS5BNNB2WEL2JONZXKZKDN5WW2ZLOOQXTKMRRG43TGOJZHA32M4TFMFZW63VHNVSW45DJN5XKKZLWMVXHJLTGN5XXIZLSL5QW4ZDSN5UWI>. Download it today! You are receiving this because you were mentioned.Message ID: ***@***.***>

[bentaculum]

It might be that the max_distance slider isn't exposed yet in the trackmate interface to trackastra. Maybe @tinevez can help here? Alternatively, you might want to give it a try with our trackastra napari plugin, max_distance is exposed there.

[gopher-confocal]

Thank you, bentaculum. No, I don't see any parameter adjustments in the FIJI TrackMate-Trackastra plugin. This was for a FIJI cell tracking workshop, which I gave Thursday, Aug. 13 and I had to resort to the LAP tracker since I could not get Trackastra to work consistently. *UIC Image Analysis Office Hours:* Mondays 9 - 10:30 AM, Jackson Hall, rm. 1-153 Mondays 2 - 3:30 PM, Snyder Hall, rm. 23 Fridays 9 - 10:30 AM, CCRB, rm. 1-220 **Any work utilizing UIC equipment or staff support must acknowledge the University Imaging Centers in publications and presentations. SCR 020997**

…

________________________________________________ Mary E. Brown, Pharm.D. Imaging Specialist/Research Professional 3/Lead Image Data Analyst University Imaging Centers Snyder Hall, rm. 23F 1475 Gortner Avenue Saint Paul, MN 55108 Email: ***@***.*** Phone: 773-458-3090

On Fri, Aug 14, 2026 at 7:34 AM Benjamin Gallusser ***@***.***> wrote: *bentaculum* left a comment (weigertlab/trackastra#69) <#69 (comment)> It might be that the max_distance slider isn't exposed yet in the trackmate interface to trackastra. Maybe @tinevez <https://github.com/tinevez> can help here? Alternatively, you might want to give it a try with our trackastra napari plugin <https://github.com/weigertlab/napari-trackastra>, max_distance is exposed there. — Reply to this email directly, view it on GitHub <#69?email_source=notifications&email_token=AMB72WAKNCBZM6OX2SX6PET5J4BOVA5CNFSNUABFM5UWIORPF5TWS5BNNB2WEL2JONZXKZKDN5WW2ZLOOQXTKMRZGMZTGOBWGI4KM4TFMFZW63VHNVSW45DJN5XKKZLWMVXHJLDGN5XXIZLSL5RWY2LDNM#issuecomment-5293338628>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AMB72WECZVKMEJ3VSDYGFOD5J4BOVAVCNFSNUABFKJSXA33TNF2G64TZHM3TMOJRGQ3DMMBXHNEXG43VMU5TKMBWGEYTSMZVGQ3KC5QC> . Triage notifications, keep track of coding agent tasks and review pull requests on the go with GitHub Mobile for iOS <https://github.com/notifications/mobile/ios/AMB72WFK6YT7K6CMBMH7Q635J4BOVA5CNFSNUABFM5UWIORPF5TWS5BNNB2WEL2JONZXKZKDN5WW2ZLOOQXTKMRZGMZTGOBWGI4KM4TFMFZW63VHNVSW45DJN5XKKZLWMVXHJKTGN5XXIZLSL5UW64Y> and Android <https://github.com/notifications/mobile/android/AMB72WDB2MDNNYFCT4K7EED5J4BOVA5CNFSNUABFM5UWIORPF5TWS5BNNB2WEL2JONZXKZKDN5WW2ZLOOQXTKMRZGMZTGOBWGI4KM4TFMFZW63VHNVSW45DJN5XKKZLWMVXHJLTGN5XXIZLSL5QW4ZDSN5UWI>. Download it today! You are receiving this because you were mentioned.Message ID: ***@***.***>

[tinevez]

Sorry for this I was away. Yes the Fiji version lags behind the latest Trackastra.
I will do my best to fix this.

[gopher-confocal]

Thanks a million, Jean-Yves! *UIC Image Analysis Office Hours:* Mondays 9 - 10:30 AM, Jackson Hall, rm. 1-153 Mondays 2 - 3:30 PM, Snyder Hall, rm. 23 Fridays 9 - 10:30 AM, CCRB, rm. 1-220 **Any work utilizing UIC equipment or staff support must acknowledge the University Imaging Centers in publications and presentations. SCR 020997**

…

________________________________________________ Mary E. Brown, Pharm.D. Imaging Specialist/Research Professional 3/Lead Image Data Analyst University Imaging Centers Snyder Hall, rm. 23F 1475 Gortner Avenue Saint Paul, MN 55108 Email: ***@***.*** Phone: 773-458-3090

On Fri, Aug 14, 2026 at 9:05 AM Jean-Yves Tinevez ***@***.***> wrote: *tinevez* left a comment (weigertlab/trackastra#69) <#69 (comment)> Sorry for this I was away. Yes the Fiji version lags behind the latest Trackastra. I will do my best to fix this. — Reply to this email directly, view it on GitHub <#69?email_source=notifications&email_token=AMB72WGQDJBMOWRLZURVXA35J4MCZA5CNFSNUABFM5UWIORPF5TWS5BNNB2WEL2JONZXKZKDN5WW2ZLOOQXTKMRZGQZDCNRRGIZKM4TFMFZW63VHNVSW45DJN5XKKZLWMVXHJLDGN5XXIZLSL5RWY2LDNM#issuecomment-5294216122>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AMB72WEKS5A4DDGBTGTUW7T5J4MCZAVCNFSNUABFKJSXA33TNF2G64TZHM3TMOJRGQ3DMMBXHNEXG43VMU5TKMBWGEYTSMZVGQ3KC5QC> . Triage notifications, keep track of coding agent tasks and review pull requests on the go with GitHub Mobile for iOS <https://github.com/notifications/mobile/ios/AMB72WCQCBQZDV4JWY43UOT5J4MCZA5CNFSNUABFM5UWIORPF5TWS5BNNB2WEL2JONZXKZKDN5WW2ZLOOQXTKMRZGQZDCNRRGIZKM4TFMFZW63VHNVSW45DJN5XKKZLWMVXHJKTGN5XXIZLSL5UW64Y> and Android <https://github.com/notifications/mobile/android/AMB72WFIHAYZIGQKAM4RGML5J4MCZA5CNFSNUABFM5UWIORPF5TWS5BNNB2WEL2JONZXKZKDN5WW2ZLOOQXTKMRZGQZDCNRRGIZKM4TFMFZW63VHNVSW45DJN5XKKZLWMVXHJLTGN5XXIZLSL5QW4ZDSN5UWI>. Download it today! You are receiving this because you were mentioned.Message ID: ***@***.***>

[tinevez]

Hello @gopher-confocal

I just released and uploaded TrackMate-Trackastra v2.1.0, that includes the max-distance parameter. You can get it by updating Fiji.

As far as I could judge the parameter is taken into account in the tracking results, but I still see weird links on your data:

They appear consistently regardless of the tracking parameters. I suspect that the issue is within the TrackMate integration, but I would like to confirm this before diving into the code. Can I ask you to run the exact tracking process with your data in the napari integration of Trackastra? And let me know whether the links are there or not?
Thanks!

[gopher-confocal]

I cannot get the napari-trackastra plugin to recognize my label images in the "Masks" option in the plugin. My label images in tiff format are recognized in the "Images" option instead. What format do the label images need to be in for recognition into the "Masks" option? Thank you for your help!