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mastodon-sc / mastodon

Mastodon – a large-scale tracking and track-editing framework for large, multi-view images.
BSD 2-Clause "Simplified" License
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project with .xml pointing on TIFF series is not opening #293

Closed xulman closed 1 month ago

xulman commented 8 months ago

... fails openning:

Snímek obrazovky 2024-03-12 182901

Some hard-coded casting of SpimData somewhere??

after converting the data into .hdf5, it went well.....

I know tiffs in conjunction with the .xml are considered evil (as they lack the features to foster a smooth viewing XP), but the same .xml file works well in plain BDV and even (!) opens the tiffs sufficienty fast (as they are small 2D images...)

xulman commented 8 months ago

(and I needed to open the image data, DUMMY wouldn't be enough.. as the ch02 contains masks that I convert to spots-detections, and then track-link using Mastodon... and then export back to CTC format)

tinevez commented 8 months ago

Hello. I cannot reproduce the problem with the beta-29. I used the 'mitosis.tiff' example in Fiji, saved to my Desktop on Mac. Re-opening the project works, provided that the TIFF file has been saved somewhere on the computer.

Screenshot 2024-03-13 at 17 02 36
tinevez commented 6 months ago

Hello @xulman Shall we pursue investigating this bug? I could not reproduce it but maybe I am not following the right way to do so.

xulman commented 6 months ago

This was really about having xml+tiff dataset (in contrast to the xml+n5 or xml+hdf5). I'll check again against the latest beta-30 and either report here (and share example failing data) or close it here.

xulman commented 6 months ago

I actually haven't checked plain tiff in Fiji, I mean the variant Mastodon opened on the currently opened image in Fiji

tinevez commented 1 month ago

Works now.