Feature "Spot intensity" calculation error

[mastodon-sc]

Feature "Spot intensity" calculation error

[drchrisch]

Yes, solved. That's it for me and I will close the issue.

[tinevez]

Hello @drchrisch

Not super recently this is suspect.

Can share the image and the files?

[drchrisch]

Sharing image is a bit difficult, I could send a link to the mastodon file.
The procedure is a follows: I load the two-channel bdv image set, run tracking detection and linking on channel 1, start feature computation, then I (without reloading) repeat tracking and linking but now on channel 2, feature computation then gives the error just as shown above.

[tinevez]

Ok I will try to reproduce. Thanks for the procedure.

[tinevez]

Hello @drchrisch
Well I could not reproduce with a 2-channel image I have at hand. I would need the image, or even a portion of it small enough to reproduce the error. If it is very big you can use our FEX instance to send it to me (see your PMs).

[drchrisch]

Well, 200 MB is not that small. Sorry, silly question, but how does this FEX works and how do I restrict access to the data?

[tinevez]

Email me please.

…

On Thu, Feb 10, 2022, 18:44 drchrisch ***@***.***> wrote: Well, 200 MB is not that small. Sorry, silly question, but how does this FEX works and how do I restrict access to the data? — Reply to this email directly, view it on GitHub <#143 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AA3KZY25TPXZ3SYAFSQGAVLU2P2OFANCNFSM5OA252EA> . Triage notifications on the go with GitHub Mobile for iOS <https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675> or Android <https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub>. You are receiving this because you commented.Message ID: ***@***.***>

[tinevez]

@drchrisch Thank you for the data.
I could open it and test Mastodon with it.
But I could not reproduce the error. When I start from scratch and do detection with sensible parameters, I have no bug. When I try to compute features on your Mastodon file, again I have no error.
So I have to ask, what is the version of mastodon you use?

[drchrisch]

That's really weird, but matches expectation. I had this problem on two computers (Windows) with Fiji.app/jars/mastodon-1.0.0-beta-20.jar.

[tinevez]

Ok we run the same. Can you give me the parameters with which you run the detection and linking steps?

[drchrisch]

DoG (diameter 4.0, threshold 100), simple LAP (15, 15, 2) (there should be a *.mastodon file as well?).

[tinevez]

Yes. And the mastodon file does not give an error :)
this is interesting.

[tinevez]

Yes I got the bug! On the 2nd channel results.

[drchrisch]

Cool! It's all in the data, right?

[tinevez]

Could you try to replace the core mastodon .jar file in your Fiji.app/jars by this one?
https://dl.pasteur.fr/fop/8R1jRnNN/mastodon-1.0.0-beta-22-SNAPSHOT.jar

[drchrisch]

Great, looks conving. Many thanks!

[tinevez]

So the bug is fixed? If yes I will do a release but not immediately.