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.

Sign up for GitHub

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

Jump to bottom

Pix preprocessing #579

Merged
merged 23 commits into from
Jun 9, 2022
Merged

Pix preprocessing #579

merged 23 commits into from
Jun 9, 2022

Commits on May 31, 2022

  1. add channel normalization

    @ngreenwald
    ngreenwald committed May 31, 2022
    Configuration menu
    Copy the full SHA
    5c034cb View commit details
    Browse the repository at this point in the history

  2. add pixel rowsum normalization

    @ngreenwald
    ngreenwald committed May 31, 2022
    Configuration menu
    Copy the full SHA
    2f5146a View commit details
    Browse the repository at this point in the history

  3. add new arg to test functions

    @ngreenwald
    ngreenwald committed May 31, 2022
    Configuration menu
    Copy the full SHA
    8612d9a View commit details
    Browse the repository at this point in the history

  4. Add testing for new pixel matrix preprocessing with channel and pixel… 

    … normalization
    @alex-l-kong
    alex-l-kong committed May 31, 2022
    Configuration menu
    Copy the full SHA
    3fbf11e View commit details
    Browse the repository at this point in the history

  5. Add documentation for calculate_pixel_intensity_percentile

    @alex-l-kong
    alex-l-kong committed May 31, 2022
    Configuration menu
    Copy the full SHA
    a04633b View commit details
    Browse the repository at this point in the history

  6. Need to account for all-zero channels in calculate_channel_percentiles

    @alex-l-kong
    alex-l-kong committed May 31, 2022
    Configuration menu
    Copy the full SHA
    e350753 View commit details
    Browse the repository at this point in the history

  7. Missing argument in docstring of calculate_pixel_intensity_percentile

    @alex-l-kong
    alex-l-kong committed May 31, 2022
    Configuration menu
    Copy the full SHA
    d1c6848 View commit details
    Browse the repository at this point in the history

Commits on Jun 1, 2022

  1. Merge branch 'master' into pix_preprocessing

    @alex-l-kong
    alex-l-kong authored Jun 1, 2022
    Configuration menu
    Copy the full SHA
    b8366ee View commit details
    Browse the repository at this point in the history

  2. Accidental uppercase 's' in 'TIFs' for test_calculate_channel_percent… 

    …ages
    @alex-l-kong
    alex-l-kong committed Jun 1, 2022
    Configuration menu
    Copy the full SHA
    08f0ffc View commit details
    Browse the repository at this point in the history

  3. Merge branch 'master' into pix_preprocessing

    @ngreenwald
    ngreenwald authored Jun 1, 2022
    Configuration menu
    Copy the full SHA
    b1cdf1d View commit details
    Browse the repository at this point in the history

  4. First round of comments addressed

    @alex-l-kong
    alex-l-kong committed Jun 1, 2022
    Configuration menu
    Copy the full SHA
    e05efae View commit details
    Browse the repository at this point in the history

  5. Merge branch 'pix_preprocessing' of https://github.com/angelolab/ark-… 

    …analysis into pix_preprocessing
    @alex-l-kong
    alex-l-kong committed Jun 1, 2022
    Configuration menu
    Copy the full SHA
    596265d View commit details
    Browse the repository at this point in the history

  6. Change addition test in test_create_fov_pixel_data to test row sums to 1

    @alex-l-kong
    alex-l-kong committed Jun 1, 2022
    Configuration menu
    Copy the full SHA
    643d551 View commit details
    Browse the repository at this point in the history

Commits on Jun 2, 2022

  1. Add test to check pixel_norm_val filtering works as intended

    @alex-l-kong
    alex-l-kong committed Jun 2, 2022
    Configuration menu
    Copy the full SHA
    47fef3b View commit details
    Browse the repository at this point in the history

Commits on Jun 3, 2022

  1. Merge branch 'master' into pix_preprocessing

    @alex-l-kong
    alex-l-kong authored Jun 3, 2022
    Configuration menu
    Copy the full SHA
    7e68aae View commit details
    Browse the repository at this point in the history

Commits on Jun 8, 2022

  1. add more testing

    @ngreenwald
    ngreenwald committed Jun 8, 2022
    Configuration menu
    Copy the full SHA
    749f0a9 View commit details
    Browse the repository at this point in the history

Commits on Jun 9, 2022

  1. Merge branch 'master' into pix_preprocessing

    @ngreenwald
    ngreenwald authored Jun 9, 2022
    Configuration menu
    Copy the full SHA
    373d704 View commit details
    Browse the repository at this point in the history

  2. switch to dataframe

    @ngreenwald
    ngreenwald committed Jun 9, 2022
    Configuration menu
    Copy the full SHA
    4a33544 View commit details
    Browse the repository at this point in the history

  3. standardize with feather files, switch naming

    @ngreenwald
    ngreenwald committed Jun 9, 2022
    Configuration menu
    Copy the full SHA
    ecca8f9 View commit details
    Browse the repository at this point in the history

  4. update tests

    @ngreenwald
    ngreenwald committed Jun 9, 2022
    Configuration menu
    Copy the full SHA
    e2855ea View commit details
    Browse the repository at this point in the history

  5. make test less stringent

    @ngreenwald
    ngreenwald committed Jun 9, 2022
    Configuration menu
    Copy the full SHA
    7298906 View commit details
    Browse the repository at this point in the history

  6. change default name in notebook

    @ngreenwald
    ngreenwald committed Jun 9, 2022
    Configuration menu
    Copy the full SHA
    47a5609 View commit details
    Browse the repository at this point in the history

  7. remove extra arg

    @ngreenwald
    ngreenwald committed Jun 9, 2022
    Configuration menu
    Copy the full SHA
    7984f57 View commit details
    Browse the repository at this point in the history