EPR
Exhaustive Photon Restoration
There are three main programs involved in 3D Deconvolution: preppsf, prepdata, and epr_i2i.
preppsf prepares the psf for epr_i2i.
prepdata prepares the data for epr_i2i.
epr_i2i performs the 3D deconvolution.
preppsf
Run the command for full option list: preppsf -h
NAME
preppsf - prepares a 3-D point spread function (psf) image data set, acquired using a Digital Imaging (light) Microscope, for use with image restoration/3-D reconstruction. Normally psf images are first processed using prepdata (see below) to apply basic corrections and any background corrections, but not temporal corrections.
SYNOPSIS
preppsf [options] before-image after-image
DESCRIPTION
preppsf performs further corrections on a psf image data set based on the fluorescence D.I.M image formation/acquisition model. The before- image argument is the name of a 3-D psf image set, acquired (DIM-1, DIM-2, CELLscan, UFM, or other) and processed using prepdata (see below) without the -norm option. The psf is extracted as a symmetric sub-region (square in XY) centered at the psf origin (-center), optionally normalized for constant total intensity (-norm), and optionally masked (-mask) to exclude any extramural data. The after-image argument is the file name for the processed psf image set. All options must precede input/output image files
Important Information
- Numerical Aperture of the objective.
- Index of refraction of immersion medium.
- Effective Pixel Size at the object in micrometers/pixel
- DIstance Spacing among Z planes in micrometers.
Example Usage
preppsf -NA 1.4 -n 1.515 -size 0.187 -spaced 0.25 -norm infocus -mask 1 psf_in psf_out
prepdata
Run the command for full option list: prepdata -h
NAME
prepdata - prepares a 2-D, 3-D or 4-D image data sets, acquired using a Digital Imaging (light) Microscope, for further processing (e.g. image restoration/3-D reconstruction)
SYNOPSIS
prepdata [options] before-image after-image
DESCRIPTION
prepdata performs all necessary corrections on a image data set based on the fluorescence D.I.M image formation/acquisition model, and can be used to perform basic imaging corrections to many forms of digitally acquired image data. The before-image argument is the name of a 3-D image set as acquired (DIM-1, DIM-2, CELLscan, UFM, or other). The after-image argument is the file name for the corrected image set, ready for further processing. The normal order of application of corrections (see -before) is basic[->background[->temporal]]. All calculations are performed using single-precision floating-point arithmetic. All options must precede input and output image file names.
epr_i2i
Run the command for full option list: epr_i2i -h
NAME
epr_i2i - Exhaustive Photon Replacement (EPR) restores contrast by removing residual out-of-focus light and improves resolution while maintaining numerical accuracy of 3-D images of specimens obtained with serial optical sectioning from wide-field or confocal light microscopy.
SYNOPSIS
epr_i2i [options] before-image[.i2i] after-image[.i2i]
DESCRIPTION
epr performs regularized, iterative image restoration with a non- negativity constraint. The before-image is a three dimensional (3-D) TIFF image composed of rectangular, regularly spaced, optical sections. Large images are decomposed into smaller, overlapping (in x and y only) image segments for restoration, and the restored segments are recomposed. The after-image is the restored 3-D image. All options must appear before the image file names, but the order of options is not important.
Example Usage
epr -psf mypsf_ -smoothness 0.0005 -iterations 250 mycell_ mycell_r