Command Line Interface¶
If you installed pycudadecon using conda, the original binaries for OTF
generation (radialft) and deconvolution (cudadecon) will also be
installed in your conda environment. The CLI is not created by pycudadecon;
it is entirely defined by cudadecon.
cudadecon¶
The cudadecon 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
cudadecon /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
cudadecon /folder/of/images 488nm /path/to/488nm_otf.tif -z 0.3 -D 31.5 -M 0 0 1
Run cudadecon --help at the command prompt for the full menu of options.
(the output below may be slightly out of date)
$ cudadecon -h
cudaDeconv. Version: 0.7.0
:
--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 positive 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
--dcbds If deskewing, do it after decon;
require sample-scan PSF and non-RA 3D OTF
--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 suppress 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 cudaDecon (or a 3D OTF file if
–3Dout is specified).
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
-3 [ --3Dout ] Output 3D, instead of rotationally averaged, OTF
-h [ --help ] produce help message