EPR

Exhaustive Photon Restoration

There are three main programs involved in 3D Deconvolution: preppsf, prepdata, and epr_i2i. They all use our own i2i image format.

preppsf prepares the psf for epr_i2i.

prepdata prepares the images 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