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Vector-optics birefringence reconstruction prototype #170

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Vector-optics birefringence reconstruction prototype #170

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talonchandler
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@talonchandler talonchandler commented Jun 17, 2024 •
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talonchandler and others added 8 commits April 23, 2024 14:25
@talonchandler @ieivanov
Phase reconstruction is invariant to voxel-size (#164)
4a20aeb 
* fix bug finding focus in stack with only one slice

* refactor for clarify

* formatting

* print -> warnings.warn

* test single-slice case

* fix test bugs

* z-scale-invariant test object

* no rescaling on output

* forward simulation takes a "brightness" - simulating real microscope

* fix example script

* add background parameter for fluorescence forward model

* test voxel-size invariance

* rename I_norm -> direct_intensity

* refactor to clarify discretization factor

* remove comment

* fix fluorescence example bug

* improved docsring

---------

Co-authored-by: Ivan Ivanov <[email protected]>
@talonchandler
poster scripting
f662aaa
@talonchandler
may 14 poster draft
945dbcb
@talonchandler
last-minute poster changes
05db85d
@talonchandler
quick clearning
15d2fbd
@talonchandler
checkpoint before svd refactor
6034cbb
@talonchandler
SVD refactor
592675d
@talonchandler
pass singular system
0fa4bbe
Base automatically changed from alg-dev to main July 5, 2024 20:52
@talonchandler
update visualization script
63dd98c
@talonchandler
Merge branch 'main' into vector-prototype
546ed16
@talonchandler
fix visualization script scaling
96d8b85
@talonchandler
correct phase recon regression, legacy recon assumes axially even gre…
005ea54 
…en's function
@talonchandler
helper functions
4034ce3
@talonchandler
fluorescence wrap safety
2e155fe
@talonchandler
3d phase wrap safety
783b916
@talonchandler
fix axial nyquist bug
55f8e5a
@talonchandler
2d phase wrap safety
22a059b
@talonchandler
fix interaction between padding and wrap safety
7c7f2a5
@talonchandler
clean defaults
a977bfe
@talonchandler
Merge branch 'wrap-safe-transfer-functions' into vector-prototype
5039a7d
@talonchandler
refactor singular system computation
6562ce7
@talonchandler
remove accidental duplicate
242ceca
@talonchandler
refactor visuals
bbe8935
@talonchandler
fix warnings from tensoring a tensor
ca4e7c5
@talonchandler
match defaults
2745005
@talonchandler
readme type
6143b6a
@talonchandler
handle napari dependency
f8d6b0c
@talonchandler
Revert "fix warnings from tensoring a tensor"
790df57 
This reverts commit ca4e7c5.
@talonchandler
Reapply "fix warnings from tensoring a tensor"
6fa39fd 
This reverts commit 790df57.
@talonchandler talonchandler mentioned this pull request Oct 16, 2024
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@talonchandler @mattersoflight