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PSF measurement, simulation, and deconvolution #130

Merged
merged 61 commits into from
Aug 13, 2024
Merged

PSF measurement, simulation, and deconvolution #130

merged 61 commits into from
Aug 13, 2024

Commits on Jan 25, 2024

  1. Create measure_psf.py

    @ieivanov
    ieivanov committed Jan 25, 2024
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Commits on Jan 27, 2024

  1. partial psf analysis report

    @ieivanov
    ieivanov committed Jan 27, 2024
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Commits on Jan 29, 2024

  1. update psf analysis report

    @ieivanov
    ieivanov committed Jan 29, 2024
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Commits on Jan 30, 2024

  1. refactor psf analysis

    @ieivanov
    ieivanov committed Jan 30, 2024
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Commits on Jan 31, 2024

  1. refactor psf analysis report

    @ieivanov
    ieivanov committed Jan 31, 2024
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Commits on Feb 3, 2024

  1. add report on deskewed data

    @ieivanov
    ieivanov committed Feb 3, 2024
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  2. initial psf simulations

    @talonchandler
    talonchandler committed Feb 3, 2024
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Commits on Feb 8, 2024

  1. GPU peak detection with torch (#129) 

    * GPU peak detection with torch

* update bead detector

* update psf measurement script

* style

---------

Co-authored-by: Ivan Ivanov <[email protected]>
    @ziw-liu @ieivanov
    ziw-liu and ieivanov authored Feb 8, 2024
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  2. ignore psf analysis warnings

    @ieivanov
    ieivanov committed Feb 8, 2024
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Commits on Feb 14, 2024

  1. update script with acquisition settings

    @ieivanov
    ieivanov committed Feb 14, 2024
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  2. better paths formatting

    @ieivanov
    ieivanov committed Feb 14, 2024
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  3. better paths formatting

    @ieivanov
    ieivanov committed Feb 14, 2024
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Commits on Feb 16, 2024

  1. update measurement script

    @ieivanov
    ieivanov committed Feb 16, 2024
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Commits on Feb 28, 2024

  1. add html report title

    @ieivanov
    ieivanov committed Feb 28, 2024
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Commits on Mar 20, 2024

  1. update psf analysis scripts

    @ieivanov
    ieivanov committed Mar 20, 2024
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Commits on May 5, 2024

  1. Merge branch 'measure_psf' into simulate-psf

    @talonchandler
    talonchandler committed May 5, 2024
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Commits on May 6, 2024

  1. typo

    @talonchandler
    talonchandler committed May 6, 2024
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  2. update dependencies

    @talonchandler
    talonchandler committed May 6, 2024
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  3. larger PSF area

    @talonchandler
    talonchandler committed May 6, 2024
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  4. main fitting script

    @talonchandler
    talonchandler committed May 6, 2024
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Commits on May 7, 2024

  1. simple_psf iteration

    @talonchandler
    talonchandler committed May 7, 2024
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  2. deconvolution prototype

    @talonchandler
    talonchandler committed May 7, 2024
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  3. settings

    @talonchandler
    talonchandler committed May 7, 2024
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  4. cutsom patch size

    @talonchandler
    talonchandler committed May 7, 2024
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  5. deconvolve CLI

    @talonchandler
    talonchandler committed May 7, 2024
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  6. psf-from-beads CLI

    @talonchandler
    talonchandler committed May 7, 2024
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  7. cli boilerplate

    @talonchandler
    talonchandler committed May 7, 2024
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Commits on May 15, 2024

  1. update psf measurement scripts

    @ieivanov
    ieivanov committed May 15, 2024
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Commits on May 17, 2024

  1. first-pass characterize

    @talonchandler
    talonchandler committed May 17, 2024
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  2. fix css issue

    @talonchandler
    talonchandler committed May 17, 2024
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Commits on May 21, 2024

  1. Merge branch 'main' into measure_psf

    @ieivanov
    ieivanov committed May 21, 2024
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Commits on May 29, 2024

  1. napari-psf-analysis is breaking fresh installations

    @talonchandler
    talonchandler committed May 29, 2024
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  2. auto-open webbrowser

    @talonchandler
    talonchandler committed May 29, 2024
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  3. handle negative with ints and clips

    @talonchandler
    talonchandler committed May 29, 2024
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  4. pass in axis labels

    @talonchandler
    talonchandler committed May 29, 2024
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Commits on May 30, 2024

  1. average beads over multiple FOVs

    @talonchandler
    talonchandler committed May 30, 2024
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Commits on Jul 2, 2024

  1. adding WIP changes, used for most recent deconvolutions

    @talonchandler
    talonchandler committed Jul 2, 2024
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  2. Merge branch 'measure_psf' into simulate-psf

    @ieivanov
    ieivanov committed Jul 2, 2024
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Commits on Jul 31, 2024

  1. style

    @ieivanov
    ieivanov committed Jul 31, 2024
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  2. Merge branch 'main' into simulate-psf

    @ieivanov
    ieivanov committed Jul 31, 2024
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  3. add napari-psf-analysis dependency

    @ieivanov
    ieivanov committed Jul 31, 2024
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Commits on Aug 1, 2024

  1. refactor characterize cli

    @ieivanov
    ieivanov committed Aug 1, 2024
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  2. more characterize refactor

    @ieivanov
    ieivanov committed Aug 1, 2024
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  3. use characterize_peaks in measure_psf

    @ieivanov
    ieivanov committed Aug 1, 2024
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  4. clean up measure_psf analysis portion

    @ieivanov
    ieivanov committed Aug 1, 2024
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  5. bugfix

    @ieivanov
    ieivanov committed Aug 1, 2024
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Commits on Aug 5, 2024

  1. delete unused scripts

    @talonchandler
    talonchandler committed Aug 5, 2024
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  2. remove unused _deskew_matrix

    @talonchandler
    talonchandler committed Aug 5, 2024
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  3. test for incorrectlyt shifted deskew

    @talonchandler
    talonchandler committed Aug 5, 2024
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  4. correct typo in test

    @talonchandler
    talonchandler committed Aug 5, 2024
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Commits on Aug 6, 2024

  1. fix deskew regression

    @talonchandler
    talonchandler committed Aug 6, 2024
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  2. style

    @talonchandler
    talonchandler committed Aug 6, 2024
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Commits on Aug 7, 2024

  1. extend O3 scan range

    @ieivanov
    ieivanov committed Aug 7, 2024
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  2. Update measure_psf.py

    @ieivanov
    ieivanov committed Aug 7, 2024
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  3. fix overflow bug

    @ieivanov
    ieivanov committed Aug 7, 2024
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  4. Update measure_psf.py

    @ieivanov
    ieivanov committed Aug 7, 2024
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  5. style

    @ieivanov
    ieivanov committed Aug 7, 2024
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  6. cleanup

    @ieivanov
    ieivanov committed Aug 7, 2024
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Commits on Aug 8, 2024

  1. rename psf functions

    @ieivanov
    ieivanov committed Aug 8, 2024
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Commits on Aug 13, 2024

  1. Update mantis/cli/characterize_psf.py 

    Co-authored-by: Talon Chandler <[email protected]>
    @ieivanov @talonchandler
    ieivanov and talonchandler authored Aug 13, 2024
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  2. Update mantis/cli/estimate_psf.py 

    Co-authored-by: Talon Chandler <[email protected]>
    @ieivanov @talonchandler
    ieivanov and talonchandler authored Aug 13, 2024
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