Command Line Interface#
If you installed pycudadecon using conda, the original binaries for OTF
generation (radialft) and deconvolution (cudaDeconv) will also be
installed in your conda environment.
cudaDeconv#
The cudaDeconv command runs deconvolution (with deskewing and rotation if
desired) on all of the files in the --input-dir whose names match the
pattern --filename-pattern, using the OTF specified by --otf-arg.
Examples#
# deconvolve a folder of images
cudaDeconv /folder/of/images 488nm /path/to/488nm_otf.tif -z 0.3
# a typical lattice experiment might also add the deskew flag and maybe MIPs
cudaDeconv /folder/of/images 488nm /path/to/488nm_otf.tif -z 0.3 -D 31.5 -M 0 0 1
Run cudaDeconv --help at the command prompt for the full menu of options
$ cudaDeconv -h
cudaDeconv compiled for LLSpy. Version: 0.4.0
--input-dir arg Folder of input images
--filename-pattern arg File name pattern to find input images
to process
--otf-file arg OTF file
--drdata arg (=0.104) Image x-y pixel size (um)
-z [ --dzdata ] arg (=0.25) Image z step (um)
--drpsf arg (=0.104) PSF x-y pixel size (um)
-Z [ --dzpsf ] arg (=0.1) PSF z step (um)
-l [ --wavelength ] arg (=0.525) Emission wavelength (um)
-W [ --wiener ] arg (=-1) Wiener constant (regularization
factor); if this value is postive then
do Wiener filter instead of R-L
-b [ --background ] arg (=90) User-supplied background
-e [ --napodize ] arg (=15) # of pixels to soften edge with
-E [ --nzblend ] arg (=0) # of top and bottom sections to blend
in to reduce axial ringing
-d [ --dupRevStack ] Duplicate reversed stack prior to decon
to reduce Z ringing
-n [ --NA ] arg (=1.2) Numerical aperture
-i [ --RL ] arg (=15) Run Richardson-Lucy, and set how many
iterations
-D [ --deskew ] arg (=0) Deskew angle; if not 0.0 then perform
deskewing before deconv
--padval arg (=0) Value to pad image with when deskewing
-w [ --width ] arg (=0) If deskewed, the output image's width
-x [ --shift ] arg (=0) If deskewed, the output image's extra
shift in X (positive->left
-R [ --rotate ] arg (=0) Rotation angle; if not 0.0 then perform
rotation around y axis after deconv
-S [ --saveDeskewedRaw ] Save deskewed raw data to files
-C [ --crop ] arg Crop final image size to [x1:x2, y1:y2,
z1:z2]; takes 6 integers separated by
space: x1 x2 y1 y2 z1 z2;
-M [ --MIP ] arg Save max-intensity projection along x,
y, or z axis; takes 3 binary numbers
separated by space: 0 0 1
-m [ --rMIP ] arg Save max-intensity projection of raw
deskewed data along x, y, or z axis;
takes 3 binary numbers separated by
space: 0 0 1
-u [ --uint16 ] Save result in uint16 format; should be
used only if no actual decon is
performed
-a [ --DoNotAdjustResForFFT ] Don't change data resolution size.
Otherwise data is cropped to perform
faster, more memory efficient FFT: size
factorable into 2,3,5,7)
--Pad arg (=0) Pad the image data with mirrored values
to avoid edge artifacts. Currently only
enabled when rotate and deskew are
zero.
--LSC arg Lightsheet correction file
--FlatStart Start the RL from a guess that is a
flat image filled with the median image
value. This may supress noise.
-p [ --bleachCorrection ] Apply bleach correction when running
multiple images in a single batch
--lzw Use LZW tiff compression
--skip arg (=0) Skip the first 'skip' number of files.
--no_overwrite Don't reprocess files that are already
deconvolved (i.e. exist in the GPUdecon
folder).
-Q [ --DevQuery ] Show info and indices of available GPUs
-h [ --help ] This help message.
-v [ --version ] show version and quit
radialft#
The radialft command turns a 3D PSF volume into a radially-averaged 2D
complex OTF file that can be used by cudaDeconv.
Examples#
radialft /path/to/psf_file.tif /path/to/new_otf_file.tif --fixorigin 10 --nocleanup
Run radialft --help at the command prompt for the full menu of options
$ radialft --help
--input-file arg input PSF file
--output-file arg output OTF file to write
--na arg (=1.25) NA of detection objective
--nimm arg (=1.29999995) refractive index of immersion medium
--xyres arg (=0.104000002) x-y pixel size
--zres arg (=0.104000002) z pixel size
--wavelength arg (=530) emission wavelength in nm
--fixorigin arg (=5) for all kz, extrapolate using pixels kr=1 to this
pixel to get value for kr=0
--krmax arg (=0) pixels outside this limit will be zeroed
(overwriting estimated value from NA and NIMM)
--nocleanup elect not to do clean-up outside OTF support
--background arg use user-supplied background instead of the
estimated
-h [ --help ] produce help message