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  • Nov 29 13:18
    adamltyson commented #44
  • Nov 29 13:17
    adamltyson closed #44
  • Nov 29 13:17

    adamltyson on spine_fix

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  • Nov 29 13:17

    adamltyson on master

    ensure track points ordering (#… (compare)

  • Nov 29 13:17
    adamltyson closed #46
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    adamltyson on 0.2.14

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    adamltyson on spine_fix

    Bump version: 0.2.14-rc0 → 0.2.… (compare)

  • Nov 25 18:18
    adamltyson commented #44
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    sonarcloud[bot] commented #46
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    adamltyson on region-info

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    adamltyson on fix_tests

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    adamltyson on fix_points_dim

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takacsflora
@takacsflora
image.png
Hi, I am having an issue with tracking my probe using brainreg-segment: the points are not in the image stack space (above pic: I meant to track the clear track on the left, and this is the image when changing the 3D view, appearing that the points all get put down on the 1st image of the stack).
I was wondering why this might be the case? Thank you for your help in advance!
8 replies
EnnyvanBeest
@EnnyvanBeest
Hi there,
Really love the tool, great work! Only me and a colleague ran into a few issues along the way that I'd like to share, as it might help others to implement:
  • Initially for me tracking did not work. I did not get an error message, but when my colleague tried it on her computer she saw the error message: "index X is out of bounds for axis 2 with size <X". After trying multiple re-installs, eventually it worked, and my guess is that I might have had python 3.7 installed in the cellfinder environment (brainreg), and 3.8 in NAPARI-env, which might have caused a conflict, but I can't say for sure.
  • I get very strange results if I trace in sample space; traces are in areas that they are clearly not in. The atlas/standard space gives a way more reasonable output (based on old-school eye-balling histology). I again asked my colleague to double check and she gets the same discrepancy between standard and sample space with her data. Is this known or is something wrong? Thanks in advance!
6 replies
Adam Tyson
@adamltyson
Hi all. BrainGlobe has joined https://forum.image.sc as a community partner. Going forward, please ask any BrainGlobe questions over there, tagging brainglobe and the tool you're asking about, e.g. cellfinder. This Gitter channel will no longer be monitored. Thanks!