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PSF measurement, simulation, and deconvolution #130

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PSF measurement, simulation, and deconvolution #130

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talonchandler
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@talonchandler talonchandler commented Feb 3, 2024 •
edited by ieivanov
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  • paired with this confluence page and this confluence page
  • 2024-05-07 - now includes draft CLI calls psf-from-beads which estimates an averaged PSF from a bead volume, and deconvolve which uses the estimated PSF to deconvolve

TODO:

  • update pre-commit

ieivanov and others added 30 commits January 25, 2024 13:23
@ieivanov
Create measure_psf.py
ef8872e
@ieivanov
partial psf analysis report
6b944e4
@ieivanov
update psf analysis report
62b7567
@ieivanov
refactor psf analysis
9be0c1a
@ieivanov
refactor psf analysis report
e445374
@ieivanov
add report on deskewed data
2f271b0
@talonchandler
initial psf simulations
0323047
@ziw-liu @ieivanov
GPU peak detection with torch (#129)
5f274cf 
* GPU peak detection with torch

* update bead detector

* update psf measurement script

* style

---------

Co-authored-by: Ivan Ivanov <[email protected]>
@ieivanov
ignore psf analysis warnings
05673e7
@ieivanov
update script with acquisition settings
dcb977a
@ieivanov
better paths formatting
a212579
@ieivanov
better paths formatting
77149b3
@ieivanov
update measurement script
8c36deb
@ieivanov
add html report title
822428c
@ieivanov
update psf analysis scripts
52c6f3b
@talonchandler
Merge branch 'measure_psf' into simulate-psf
9ec7cb8
@talonchandler
typo
4a8161c
@talonchandler
update dependencies
5ebe58c
@talonchandler
larger PSF area
5fe793f
@talonchandler
main fitting script
b8623fd
@talonchandler
simple_psf iteration
97c7968
@talonchandler
deconvolution prototype
15d2f59
@talonchandler
settings
fb4cc72
@talonchandler
cutsom patch size
ea6acdb
@talonchandler
deconvolve CLI
2b84fb9
@talonchandler
psf-from-beads CLI
74024e0
@talonchandler
cli boilerplate
8a0377f
@ieivanov
update psf measurement scripts
ec20b03
@talonchandler
first-pass characterize
be0c637
@talonchandler
fix css issue
6af9092
@ieivanov ieivanov changed the base branch from main to measure_psf May 28, 2024 18:23
@ieivanov ieivanov mentioned this pull request Jul 1, 2024
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@ieivanov ieivanov changed the title PSF simulation and deconvolution PSF measurement, simulation, and deconvolution Jul 2, 2024
@ieivanov ieivanov mentioned this pull request Jul 2, 2024
Closed
1 task
@ieivanov ieivanov changed the base branch from measure_psf to main July 2, 2024 21:55
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@talonchandler @ieivanov @ziw-liu