Easy to use wrapper for pycudasirecon/cudasirecon, 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.
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:
Under development
This is not yet published on conda-forge, so the installation process is fairly manual.
conda create -n pysimrecon_env python=3.12 and activate it conda activate pysimrecon_env. The environment has been called pysimrecon_env in this example but this is not a requirement.conda install -c conda-forge --file conda_requirements.txt. If there are any issues with this step, please refer to the requirements section.python -m pip install .[progress] as this includes progress bars using tqdm (simply use python -m pip install . if you don't want this).-e, i.e. python -m pip install -e .[progress].If you have any problems installing this package, please open an issue.
Calls to sim-otf and sim-recon can both take a -c/--config argument. This should be similar to the config.ini file in the configs directory, which specifies the defaults config, any per-channel configs (some values should be set on a per-channel basis), and the locations of OTFs for each channel. Channels are specified based on the emission wavelength in nanometres (must be an integer).
For a channel with an emission wavelength of 525nm:
[configs] section, the channel config can be specified as 525=/path/to/configs/525.cfg[otfs] section, the channel OTF file can be specified as 525=/path/to/otfs/525_otf.tiff
A directory can be specified within each of the [configs] and [otfs] sections. If given, files can also be defined relative to that directory, e.g. if directory=/path/to, then 525=/path/to/otfs/525_otf.tiff could simply be 525=otfs/525_otf.tiff.
Config settings will be overriden by higher-priority sources.The defaults config and per-channel configs expect the same form, with the headers [otf config] for settings that are used with sim-otf and [recon config] for settings that are used with sim-recon. For these commands, available settings can be found in their argument form (with a leading -- that should be removed for config use) in the CLI section under 'Overrides'. While these settings can be set via command line arguments, command line arguments cannot be set per-channel and will apply to all files and channels.
usage: sim-otf [-h] -p PSF_PATHS [PSF_PATHS ...] [-c CONFIG_PATH]
[-o OUTPUT_DIRECTORY] [--overwrite] [--no-cleanup]
[--shape XY_SHAPE XY_SHAPE] [--centre XY_CENTRE XY_CENTRE] [-v]
[--no-progress] [--nphases NPHASES] [--ls LS] [--na NA]
[--nimm NIMM] [--background BACKGROUND] [--beaddiam BEADDIAM]
[--angle ANGLE] [--nocompen] [--5bands]
[--fixorigin FIXORIGIN FIXORIGIN]
[--leavekz LEAVEKZ LEAVEKZ LEAVEKZ] [--I2M I2M]
SIM PSFs to OTFs
options:
-h, --help show this help message and exit
-p PSF_PATHS [PSF_PATHS ...], --psf PSF_PATHS [PSF_PATHS ...]
Paths to PSF files to be reconstructed (multiple paths
can be given)
-c CONFIG_PATH, --config-path CONFIG_PATH
Path to the root config that specifies the paths to
the OTFs and the other configs (recommended)
-o OUTPUT_DIRECTORY, --output-directory OUTPUT_DIRECTORY
If specified, the output directory in which the OTF
files will be saved (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)
--centre XY_CENTRE XY_CENTRE
Takes 2 floats (X Y), specifying the 0-indexed pixel
coordinates that PSFs are cropped around (the image
centre is used otherwise)
-v, --verbose Show more logging
--no-progress turn off progress bars (only has an effect if tqdm is
installed)
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 (default=5)
--ls LS Line spacing of SIM pattern in microns (default=0.172)
--na NA Detection objective's numerical aperture (default=1.2)
--nimm NIMM Refractive index of immersion medium (default=1.33)
--background BACKGROUND
Camera readout background (default=0)
--beaddiam BEADDIAM The diameter of the bead in microns (default=0.12)
--angle ANGLE The k0 vector angle with which the PSF is taken
(default=0)
--nocompen Do not perform bead size compensation
--5bands Output to 5 OTF bands (otherwise higher-order's real
and imaginary bands are combined into one output)
--fixorigin FIXORIGIN FIXORIGIN
The starting and end pixel for interpolation along kr
axis (default=(2, 9))
--leavekz LEAVEKZ LEAVEKZ LEAVEKZ
Pixels to be retained on kz axis (default=(0, 0, 0))
--I2M I2M I2M OTF file (input data contains I2M PSF)usage: sim-recon [-h] -d SIM_DATA_PATHS [SIM_DATA_PATHS ...] [-c CONFIG_PATH]
[-o OUTPUT_DIRECTORY] [-p PROCESSING_DIRECTORY] [--otf OTFS]
[-amc] [--type {dv,tiff}] [--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] [--otfcutoff OTFCUTOFF]
[--zoomfact ZOOMFACT] [--zzoom ZZOOM]
[--background BACKGROUND] [--usecorr USECORR]
[--forcemodamp FORCEMODAMP [FORCEMODAMP ...]]
[--k0angles K0ANGLES K0ANGLES K0ANGLES] [--otfRA]
[--otfPerAngle] [--fastSI] [--k0searchAll K0SEARCHALL]
[--norescale NORESCALE] [--equalizez] [--equalizet]
[--dampenOrder0] [--nosuppress NOSUPPRESS] [--nokz0]
[--gammaApo GAMMAAPO] [--explodefact EXPLODEFACT]
[--nofilterovlps NOFILTEROVLPS]
[--saveprefiltered SAVEPREFILTERED]
[--savealignedraw SAVEALIGNEDRAW]
[--saveoverlaps SAVEOVERLAPS] [--2lenses] [--bessel]
[--besselExWave BESSELEXWAVE] [--besselNA BESSELNA]
[--deskew DESKEW] [--deskewshift DESKEWSHIFT] [--noRecon]
[--cropXY CROPXY] [--xyres XYRES] [--zres ZRES]
[--zresPSF ZRESPSF] [--wavelength WAVELENGTH]
Reconstruct SIM data
options:
-h, --help show this help message and exit
-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)
-c CONFIG_PATH, --config-path CONFIG_PATH
Path to the root config that specifies the paths to
the OTFs and the other configs (recommended)
-o OUTPUT_DIRECTORY, --output-directory OUTPUT_DIRECTORY
If specified, the output directory in which the
reconstructed files will be saved (otherwise each
reconstruction will be saved in the same directory as
its SIM data file)
-p PROCESSING_DIRECTORY, --processing-directory PROCESSING_DIRECTORY
If specified, the directory in which the temporary
files will be stored for processing (otherwise the
output directory will be used)
--otf OTFS The OTF file for a channel can be specified, which
should be given as <emission wavelength in nm>:<the
path to the OTF file> e.g. '--otf
525:/path/to/525_otf.tiff' (argument can be given
multiple times to provide OTFs for multiple channels)
-amc, --allow-missing-channels
If specified, attempt reconstruction of other channels
in a multi-channel file if one or more are not
configured
--type {dv,tiff} File type of output images
--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)
Overrides:
Arguments that override configured values. Defaults stated are only used
if no value is given or configured.
--ndirs NDIRS Number of SIM directions (default=3)
--nphases NPHASES Number of pattern phases per SIM direction (default=5)
--nordersout NORDERSOUT
Number of output SIM orders (must be <= nphases//2;
safe to ignore usually) (default=0)
--angle0 ANGLE0 Angle of the first SIM angle in radians
(default=1.648) (depends on: k0angles is None)
--ls LS Line spacing of SIM pattern in microns (default=0.172)
--na NA Detection objective's numerical aperture (default=1.2)
--nimm NIMM Refractive index of immersion medium (default=1.33)
--wiener WIENER Wiener constant; lower value leads to higher
resolution and noise (playing with it extensively is
strongly encouraged) (default=0.01)
--otfcutoff OTFCUTOFF
OTF threshold below which it'll be considered noise
and not used in "makeoverlaps" (default=0.006)
--zoomfact ZOOMFACT Lateral zoom factor in the output over the input
images (default=2)
--zzoom ZZOOM Axial zoom factor (default=1)
--background BACKGROUND
Camera readout background (default=0)
--usecorr USECORR Use a flat-field correction file if provided
--forcemodamp FORCEMODAMP [FORCEMODAMP ...]
Force modamps to these values; useful when image
quality is low and auto-estimated modamps are below,
say, 0.1
--k0angles K0ANGLES K0ANGLES K0ANGLES
Use these pattern vector k0 angles for all directions
(instead of inferring the rest angles from angle0)
--otfRA Use rotationally averaged OTF, otherwise 3/2D OTF is
used for 3/2D raw data (default=0)
--otfPerAngle Use one OTF per SIM angle, otherwise one OTF is used
for all angles, which is how it's been done
traditionally (default=0)
--fastSI SIM image is organized in Z->Angle->Phase order,
otherwise Angle->Z->Phase image order is assumed
(default=0)
--k0searchAll K0SEARCHALL
Search for k0 at all time points (default=0)
--norescale NORESCALE
No bleach correction (default=0)
--equalizez Bleach correction for z (default=0) (depends on:
norescale != 1)
--equalizet Bleach correction for time (default=0) (depends on:
norescale != 1)
--dampenOrder0 Dampen order-0 in final assembly; do not use for 2D
SIM; good choice for high-background images
(default=0)
--nosuppress NOSUPPRESS
Do not suppress DC singularity in the result (good
choice for 2D/TIRF data) (default=0)
--nokz0 Do not use kz=0 plane of the 0th order in the final
assembly (mostly for debug) (default=0)
--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 (default=1)
--explodefact EXPLODEFACT
Artificially explode the reciprocal-space distance
between orders by this factor (for debug) (default=1)
--nofilterovlps NOFILTEROVLPS
Do not filter the overlapping region between bands
(for debug) (default=0)
--saveprefiltered SAVEPREFILTERED
Save separated bands (half Fourier space) into a file
and exit (for debug)
--savealignedraw SAVEALIGNEDRAW
Save drift-fixed raw data (half Fourier space) into a
file and exit (for debug)
--saveoverlaps SAVEOVERLAPS
Save overlap0 and overlap1 (real-space complex data)
into a file and exit (for debug)
--2lenses Toggle to indicate I5S data (default=0)
--bessel Toggle to indicate Bessel-SIM data (default=0)
--besselExWave BESSELEXWAVE
Bessel SIM excitation wavelength in microns
(default=0.488) (depends on: bessel == 1)
--besselNA BESSELNA Bessel SIM excitation NA (default=0.144) (depends on:
bessel == 1)
--deskew DESKEW Deskew angle; if not 0.0 then perform deskewing before
processing (default=0)
--deskewshift DESKEWSHIFT
If deskewed, shift the output image by this in X
(positive->left) (default=0) (depends on: deskew != 0)
--noRecon No reconstruction will be performed; useful when
combined with "deskew" (default=0)
--cropXY CROPXY Crop the X-Y dimension to this number; 0 means no
cropping (default=0)
--xyres XYRES X-Y pixel size (use metadata value by default)
--zres ZRES Z pixel size (use metadata value by default)
--zresPSF ZRESPSF Z pixel size of PSF (use "zres" value by default)
--wavelength WAVELENGTH
Emission wavelength in nm (use metadata value by
default)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)Accepts a list of DV files to be converted to TIFFs (with some OME metadata).