Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Support 3D segmentation with TrackMate-Ilastik. #3

Open
wants to merge 17 commits into
base: master
Choose a base branch
from
Open

Commits on Nov 29, 2023

  1. Configuration menu
    Copy the full SHA
    ea91196 View commit details
    Browse the repository at this point in the history
  2. Configuration menu
    Copy the full SHA
    83f3f73 View commit details
    Browse the repository at this point in the history
  3. Configuration menu
    Copy the full SHA
    bca0709 View commit details
    Browse the repository at this point in the history
  4. Configuration menu
    Copy the full SHA
    d79a0b5 View commit details
    Browse the repository at this point in the history
  5. Configuration menu
    Copy the full SHA
    571a5f0 View commit details
    Browse the repository at this point in the history
  6. Configuration menu
    Copy the full SHA
    7316dfa View commit details
    Browse the repository at this point in the history
  7. Depend now on imglib2-mesh.

    tinevez committed Nov 29, 2023
    Configuration menu
    Copy the full SHA
    c920590 View commit details
    Browse the repository at this point in the history
  8. Reword the test drive.

    tinevez committed Nov 29, 2023
    Configuration menu
    Copy the full SHA
    79db883 View commit details
    Browse the repository at this point in the history
  9. Rework the detection preview.

    We do not recompute probabilities when the frame and the ROI do
    not change. It saves a lot of time when adjusting the probability
    threshold, because ilastik takes a lot of time to launch everytime.
    Here we used the same strategy that for the Weka detector: we
    simply store the last probability map and check whether we need
    to recompute it next time the user presses the 'Preview' button.
    Nowe I have to check that it also works for 3D.
    tinevez committed Nov 29, 2023
    Configuration menu
    Copy the full SHA
    f13e9cf View commit details
    Browse the repository at this point in the history
  10. Configuration menu
    Copy the full SHA
    a70264c View commit details
    Browse the repository at this point in the history
  11. Configuration menu
    Copy the full SHA
    9f28e92 View commit details
    Browse the repository at this point in the history
  12. Minor tweak

    tinevez committed Nov 29, 2023
    Configuration menu
    Copy the full SHA
    973bce6 View commit details
    Browse the repository at this point in the history

Commits on Dec 4, 2023

  1. Configuration menu
    Copy the full SHA
    aa4fa01 View commit details
    Browse the repository at this point in the history

Commits on May 1, 2024

  1. Configuration menu
    Copy the full SHA
    1646bdd View commit details
    Browse the repository at this point in the history
  2. Add smoothing of output objects to the detector.

    Amazingly enough, it is sufficient to simply add the smoothing
    parameter to the settings maps for it to work. Indeed, the smoothing
    is handled by the threshold detector, that for ilastik, operates
    on the probability map generated by the ilastik command. So there
    is only very little to do to make it work here.
    Unexpected but pleasant.
    tinevez committed May 1, 2024
    Configuration menu
    Copy the full SHA
    f2739c3 View commit details
    Browse the repository at this point in the history
  3. Configuration menu
    Copy the full SHA
    8d16978 View commit details
    Browse the repository at this point in the history
  4. Tweak test drive.

    tinevez committed May 1, 2024
    Configuration menu
    Copy the full SHA
    d3d6456 View commit details
    Browse the repository at this point in the history