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# PySIMRecon

Easy to use wrapper for pyCUDAsirecon, allowing the use of DV (DeltaVision) files without IVE/Priism (UCSF library with MRC/DV support).

This is built for easy use from the command line or as part of an auto-processing pipeline, allowing parameters to be pre-configured or defined at runtime.

### Goal

To reconstruct the SIM data and create OTFs from PSFs from the cryoSIM at B24, Diamond from the .dv files created by Cockpit. Requirements are:

- Easy to use
- Open source
- Reproducable results
- Can be used as part of an automatic processing pipeline

### Current state

Under development

{{ SECTIONCONFIGURATION_MD }}

### CLI

##### sim-otf

```
usage: sim-otf [-c CONFIG_PATH] [-p PSF_PATHS [PSF_PATHS ...]]
[-o OUTPUT_DIRECTORY] [--overwrite] [--no-cleanup]
[--shape XY_SHAPE XY_SHAPE] [-v] [--no-progress]
[--nphases NPHASES] [--ls LS] [--na NA] [--nimm NIMM]
[--background BACKGROUND] [--beaddiam BEADDIAM] [--angle ANGLE]
[--nocompen NOCOMPEN] [--fixorigin FIXORIGIN FIXORIGIN]
[--leavekz LEAVEKZ LEAVEKZ LEAVEKZ] [-h]
SIM PSFs to OTFs
options:
-c CONFIG_PATH, --config-path CONFIG_PATH
Path to the root config that specifies the paths to
the OTFs and the other configs
-p PSF_PATHS [PSF_PATHS ...], --psf PSF_PATHS [PSF_PATHS ...]
Paths to PSF files to be reconstructed (multiple paths
can be given)
-o OUTPUT_DIRECTORY, --output-directory OUTPUT_DIRECTORY
If specified, the output directory that the OTFs will
be saved in, otherwise each OTF will be saved in the
same directory as its PSF
--overwrite If specified, files will be overwritten if they
already exist (unique filenames will be used
otherwise)
--no-cleanup If specified, files created during the OTF creation
process will not be cleaned up
--shape XY_SHAPE XY_SHAPE
Takes 2 integers (X Y), specifying the shape to crop
PSFs to before converting (powers of 2 are fastest)
-v, --verbose Show more logging
--no-progress turn off progress bars (only has an effect if tqdm is
installed)
-h, --help show this help message and exit
Overrides:
Arguments that override configured values. Defaults stated are only used
if no value is given or configured.
--nphases NPHASES Number of pattern phases per SIM direction
--ls LS Line spacing of SIM pattern in microns
--na NA Detection objective's numerical aperture
--nimm NIMM Refractive index of immersion medium
--background BACKGROUND
Camera readout background
--beaddiam BEADDIAM The diameter of the bead in microns, by default 0.12
--angle ANGLE The k0 vector angle with which the PSF is taken, by
default 0
--nocompen NOCOMPEN Do not perform bead size compensation, default False
(do perform)
--fixorigin FIXORIGIN FIXORIGIN
The starting and end pixel for interpolation along kr
axis, by default (2, 9)
--leavekz LEAVEKZ LEAVEKZ LEAVEKZ
Pixels to be retained on kz axis, by default (0, 0, 0)
```

##### sim-recon

```
usage: sim-recon [-c CONFIG_PATH] [-d SIM_DATA_PATHS [SIM_DATA_PATHS ...]]
[-o OUTPUT_DIRECTORY] [--overwrite] [--no-cleanup]
[--keep-split] [--parallel] [-v] [--no-progress]
[--ndirs NDIRS] [--nphases NPHASES] [--nordersout NORDERSOUT]
[--angle0 ANGLE0] [--ls LS] [--na NA] [--nimm NIMM]
[--wiener WIENER] [--zoomfact ZOOMFACT] [--zzoom ZZOOM]
[--background BACKGROUND] [--usecorr USECORR]
[--k0angles K0ANGLES K0ANGLES K0ANGLES] [--otfRA OTFRA]
[--otfPerAngle OTFPERANGLE] [--fastSI FASTSI]
[--k0searchAll K0SEARCHALL] [--norescale NORESCALE]
[--equalizez EQUALIZEZ] [--equalizet EQUALIZET]
[--dampenOrder0 DAMPENORDER0] [--nosuppress NOSUPPRESS]
[--nokz0 NOKZ0] [--gammaApo GAMMAAPO]
[--explodefact EXPLODEFACT] [--nofilterovlps NOFILTEROVLPS]
[--deskew DESKEW] [--deskewshift DESKEWSHIFT]
[--noRecon NORECON] [--cropXY CROPXY] [--xyres XYRES]
[--zres ZRES] [--zresPSF ZRESPSF] [--wavelength WAVELENGTH]
[-h]
Reconstruct SIM data
options:
-c CONFIG_PATH, --config-path CONFIG_PATH
Path to the root config that specifies the paths to
the OTFs and the other configs
-d SIM_DATA_PATHS [SIM_DATA_PATHS ...], --data SIM_DATA_PATHS [SIM_DATA_PATHS ...]
Paths to SIM data files to be reconstructed (multiple
paths can be given)
-o OUTPUT_DIRECTORY, --output-directory OUTPUT_DIRECTORY
The output directory to save reconstructed files in
--overwrite If specified, files will be overwritten if they
already exist (unique filenames will be used
otherwise)
--no-cleanup If specified, files created during the reconstruction
process will not be cleaned up
--keep-split If specified, channels will not be stitched back
together after reconstruction
--parallel If specified, up to 2 processes will be run at a time
-v, --verbose Show more logging
--no-progress turn off progress bars (only has an effect if tqdm is
installed)
-h, --help show this help message and exit
Overrides:
Arguments that override configured values. Defaults stated are only used
if no value is given or configured.
--ndirs NDIRS Number of SIM directions
--nphases NPHASES Number of pattern phases per SIM direction
--nordersout NORDERSOUT
Number of output SIM orders (must be <= nphases//2;
safe to ignore usually)
--angle0 ANGLE0 Angle of the first SIM angle in radians
--ls LS Line spacing of SIM pattern in microns
--na NA Detection objective's numerical aperture
--nimm NIMM Refractive index of immersion medium
--wiener WIENER Wiener constant; lower value leads to higher
resolution and noise; playing with it extensively is
strongly encouraged
--zoomfact ZOOMFACT Lateral zoom factor in the output over the input
images; leaving it at 2 should be fine in most cases
--zzoom ZZOOM Axial zoom factor; almost never needed
--background BACKGROUND
Camera readout background
--usecorr USECORR Use a flat-field correction file if provided
--k0angles K0ANGLES K0ANGLES K0ANGLES
Use these pattern vector k0 angles for all directions
(instead of inferring the rest angles from angle0)
--otfRA OTFRA Use rotationally averaged OTF; otherwise uses 3/2D OTF
for 3/2D raw data
--otfPerAngle OTFPERANGLE
Use one OTF per SIM angle; otherwise one OTF is used
for all angles, which is how it's been done
traditionally
--fastSI FASTSI SIM image is organized in Z->Angle->Phase order;
otherwise assuming Angle->Z->Phase image order
--k0searchAll K0SEARCHALL
Search for k0 at all time points
--norescale NORESCALE
No bleach correction
--equalizez EQUALIZEZ
Bleach correction for z
--equalizet EQUALIZET
Bleach correction for time
--dampenOrder0 DAMPENORDER0
Dampen order-0 in final assembly; do not use for 2D
SIM; good choice for high-background images
--nosuppress NOSUPPRESS
Do not suppress DC singularity in the result (good
choice for 2D/TIRF data)
--nokz0 NOKZ0 Do not use kz=0 plane of the 0th order in the final
assembly (mostly for debug)
--gammaApo GAMMAAPO Output apodization gamma; 1.0 means triangular apo;
lower value means less dampening of high-resolution
info at the trade-off of higher noise
--explodefact EXPLODEFACT
Artificially exploding the reciprocal-space distance
between orders by this factor (for debug)
--nofilterovlps NOFILTEROVLPS
--deskew DESKEW Deskew angle; if not 0.0 then perform deskewing before
processing
--deskewshift DESKEWSHIFT
If deskewed, the output image's extra shift in X
(positive->left)
--noRecon NORECON No reconstruction will be performed; useful when
combined with "deskew":
--cropXY CROPXY Crop the X-Y dimension to this number; 0 means no
cropping
--xyres XYRES X-Y pixel size (only used for TIFF files)
--zres ZRES Z pixel size (only used for TIFF files)
--zresPSF ZRESPSF Z pixel size (used in PSF TIFF files)
--wavelength WAVELENGTH
Emission wavelength in nm (only used for TIFF files)
```

##### otf-view

```
usage: otf-view [-h] [--show] [--show-only] [-o OUTPUT_DIRECTORY] [-v]
[--no-progress]
otf_paths [otf_paths ...]
Create OTF views
positional arguments:
otf_paths OTF file paths
options:
-h, --help show this help message and exit
--show Display the plots while running
--show-only Show plots without saving
-o OUTPUT_DIRECTORY, --output-directory OUTPUT_DIRECTORY
Save to this directory if saving plots, otherwise each
plot will be saved with its input file
-v, --verbose Show more logging
--no-progress turn off progress bars (only has an effect if tqdm is
installed)
```

##### dv2tiff

Accepts a list of DV files to be converted to TIFFs (with some OME metadata).
19 changes: 19 additions & 0 deletions docs/help/otf_view.txt
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usage: otf-view [-h] [--show] [--show-only] [-o OUTPUT_DIRECTORY] [-v]
[--no-progress]
otf_paths [otf_paths ...]

Create OTF views

positional arguments:
otf_paths OTF file paths

options:
-h, --help show this help message and exit
--show Display the plots while running
--show-only Show plots without saving
-o OUTPUT_DIRECTORY, --output-directory OUTPUT_DIRECTORY
Save to this directory if saving plots, otherwise each
plot will be saved with its input file
-v, --verbose Show more logging
--no-progress turn off progress bars (only has an effect if tqdm is
installed)
54 changes: 54 additions & 0 deletions docs/help/sim_otf.txt
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usage: sim-otf [-c CONFIG_PATH] [-p PSF_PATHS [PSF_PATHS ...]]
[-o OUTPUT_DIRECTORY] [--overwrite] [--no-cleanup]
[--shape XY_SHAPE XY_SHAPE] [-v] [--no-progress]
[--nphases NPHASES] [--ls LS] [--na NA] [--nimm NIMM]
[--background BACKGROUND] [--beaddiam BEADDIAM] [--angle ANGLE]
[--nocompen NOCOMPEN] [--fixorigin FIXORIGIN FIXORIGIN]
[--leavekz LEAVEKZ LEAVEKZ LEAVEKZ] [-h]

SIM PSFs to OTFs

options:
-c CONFIG_PATH, --config-path CONFIG_PATH
Path to the root config that specifies the paths to
the OTFs and the other configs
-p PSF_PATHS [PSF_PATHS ...], --psf PSF_PATHS [PSF_PATHS ...]
Paths to PSF files to be reconstructed (multiple paths
can be given)
-o OUTPUT_DIRECTORY, --output-directory OUTPUT_DIRECTORY
If specified, the output directory that the OTFs will
be saved in, otherwise each OTF will be saved in the
same directory as its PSF
--overwrite If specified, files will be overwritten if they
already exist (unique filenames will be used
otherwise)
--no-cleanup If specified, files created during the OTF creation
process will not be cleaned up
--shape XY_SHAPE XY_SHAPE
Takes 2 integers (X Y), specifying the shape to crop
PSFs to before converting (powers of 2 are fastest)
-v, --verbose Show more logging
--no-progress turn off progress bars (only has an effect if tqdm is
installed)
-h, --help show this help message and exit

Overrides:
Arguments that override configured values. Defaults stated are only used
if no value is given or configured.

--nphases NPHASES Number of pattern phases per SIM direction
--ls LS Line spacing of SIM pattern in microns
--na NA Detection objective's numerical aperture
--nimm NIMM Refractive index of immersion medium
--background BACKGROUND
Camera readout background
--beaddiam BEADDIAM The diameter of the bead in microns, by default 0.12
--angle ANGLE The k0 vector angle with which the PSF is taken, by
default 0
--nocompen NOCOMPEN Do not perform bead size compensation, default False
(do perform)
--fixorigin FIXORIGIN FIXORIGIN
The starting and end pixel for interpolation along kr
axis, by default (2, 9)
--leavekz LEAVEKZ LEAVEKZ LEAVEKZ
Pixels to be retained on kz axis, by default (0, 0, 0)
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