Registration page

Revision as of 16:37, 26 March 2009

Executables for Registration

There are two executables for registration, one is to register an image pair and one is to jointly register a bunch of images given the pairwise transformations.

register_pair

This executable is for registering a pair of images. Too see the useage, type "-?"

Usage:

register_pair.exe [string] [string] [-channel integer] [-bg float] [-smooth float] [-gdbicp string] 
                  [-slices integer] [-remove_2d bool] [-scaling bool]

REQUIRED:

          string  From image file
          string  To image file

Optional:

   Switch Type    Help [default value]

 -channel integer The color channel (0-red, 1-green, 2-blue), or the image channel if the original image is a 
                  lsm image. [0]
      -bg float   threshold value for the background  [30]
  -smooth float   If smoothing is performed  [0.5]
  -gdbicp string  The path where the gdbicp exe can be found. The executable of gdbicp can be found at 
                  http://www.vision.cs.rpi.edu/gdbicp 
  -slices integer Number of slices to register. Needed when registering large i mage stacks on PC.  [100]
 -scaling bool    Substantial scaling is expected.  [not set]
       -? bool    Print this message

Examples:

1. To register two lsm images, image1.lsm and image2.lsm, using all channels do (on Windows):
        regiser_pairs.exe image1.lsm image1.lsm
2. To register two lsm images, image1.lsm and image2.lsm, using channel 0 do (on Windows):
       regiser_pairs.exe image1.lsm image1.lsm -channel 0

register_joint

This executable is for registering a set of images jointly with global consistency. A list of xml files, each containing a pairwise transformation generated using regiser_pair, should be provided as the input to the executable. Too see the useage, type "-?"

Usage:

register_joint.exe [string] [-output string] [-multiplier float] [-error_bound float] [-quick bool] [-roi string]

REQUIRED:

            string  A file containing filenames of xml files, each containing a pairwise transformation.

Optional:

      Switch Type   Help [default value]

     -output string Output xml filename  ['joint_transforms.xml']
 -multiplier float  The multiplier for the error scale. 4 is a good value. It is better to tune the error_bound 
                    using this parameter. [0]
-error_bound float  The upper bound for the accepted error in the range of [-1,0]. When set to 0, all pairs are
                    accepted  [0]
      -quick bool   No mutual consistency is imposed  [not set]
        -roi string Text file containing the list of image names in the ROI  []
          -? bool   Print this message 

If -multiplier is set, pairwise transformations with higher errors are excluded in the computation.

Executables for Montaging

There is one executable for generating montages from existing transformations, and one GUI executable for navigating the montage.

mosaic_images

This executable generate the montage using a set of transformations stored in an xml file, which is either generated by register_pairwise, or register_joint. The outputs of the operation are a xml file, a 2D projection of the image montage, and a directory containing 2D image slices of the 3D image, which can also be generated upon request. All outputs have the same filename (but different extensions). If the filename not specified, it is the filename of the anchor image prefixed with montage_. To see the usage, type "-?"

Usage:

mosaic_images.exe [string] [string] [-channel integer] [-path string] [-old_str string] [-new_str string] 
                  [-output string] [-in_anchor bool] [-overlap_only bool] [-nn bool] [-blending integer]         
                  [-denoise bool]

REQUIRED:

              string  A xml file containing transformations 
              string  Anchor image name 

Optional:

       Switch Type    Help [default value]

     -channel integer The color channel (0-red, 1-green, 2-blue), or the image channel if the original image is
                      lsm image.  [0]
        -path string  The path of the image files.  ['.']
     -old_str string  The old substr in the image names to be replaced  []
     -new_str string  The new substr in the image names  []
          -3d bool    Generate a 3D image as well  [not set]
      -output string  The name of the output  []
   -in_anchor bool    The final space is set to the anchor image  [not set]
-overlap_only bool    Only consider images that overlap the anchor image  [not set]
          -nn bool    Use Nearest-Neighbor interpolation  [not set]
    -blending integer 0: max (default), 1: even weighted, 2: photopleaching weighted (the fanciest).  [0]
     -denoise bool    Making an attempt to remove noise of high frequencies  [not set]
           -? bool    Print this message

Examples:

1. To montage a set of images in the parent directory with transformations stored in joint_transforms.xml and image1.lsm as the anchor (reference) image, do

      mosaic_images joint_transforms.xml image1.lsm -path ../

If -output not specified, the montage is stored in the directory named montage_image1 and the xml file is montage_image1.xml. A 2D maximum projection is also generated and is named montage_image1_2d_proj.png in this example.

2. -old_str and -new_str can be used to change the image names recorded in the xml files. The string following -old_str is what to be replaced, and the string following -new_str is what to be replaced with. For example, if the image names in the xml file is *.lsm and the images for montaging are *.tiff, the previous example becomes

      mosaic_images joint_transforms.xml image1.tiff -path ../ -old_str .lsm -new_str .tiff

mosaic_image_pair

This executable generates a color montage for inspection of the quality of registration. The transformation can be from either pairwise or joint registration stored in an xml file. One image is displayed in green and one in red. The region of overlap should be in yellow for good alignment. The result of the operation is an xml file, a 3D image, a 2D projection, and a directory containing 2D image slices of the 3D image. All outputs have the same filename (different extensions). If the output filename not specified, it is the filename of the to_image prefixed with pairwise_montage_ . To see the usage, type "-?"

Usage:

mosaic_image_pair.exe [ string] [ string] [ string] [-channel integer] [-path string] [-old_str string] 
                      [-new_str string] [-output string] [-in_anchor bool]

REQUIRED:

           string  xml file for transforms  []
           string  From_image name  []
           string  To_image name  []

Optional:

    Switch Type    Help [default value]

  -channel integer The color channel (0-red, 1-green, 2-blue), or the image channel if the original image is 
                   lsm image.  [0]
     -path string  The path of the image files.  ['.']
  -old_str string  The old substr in the image names to be replaced  []
  -new_str string  The new substr in the image names  []
   -output string  The name of the otuput image  ['fused_image.tif']
-in_anchor bool    The output image is the size of the anchor image  [not set]
        -? bool    Print this message

MontageNavigator

To navigate the montage, load the xml of the montage generated by mosaic_images. The user can click on the montage to see the coordinates of a point in the original images. To generate cropped regions, the user has to provide the image directory which contains the montage to be cropped from. The reason for having to choose a directory when saving a cropped region is to make it possible to pick a montage directory of another channel of the same image set for cropping.

Scripts for Batch Processing

To generate a montage given image names in pairs as the input do:

  register_pairs image_dir pair_list_file

The pair_list_file contains a pair of image names per line. The script runs register_pairwse on the given pairs, register_joint using the generated pairwise transformations, and mosaic_images using the first image an the anchor. If only one image pair is provided in the input file, the montage is generated using mosaic_image_pair, which displays the two images with two different colors. Image pairs that fail to register are stored in file pair_list_file.failed_pairs.

To generate a montage given a set image names as the input do:

  regiser_list image_dir image_list_file filename_pattern

Different from register_pairs, this register_list first figures out the adjacent image pairs based on the filename_pattern. Both 1D and 2D adjacency is allowed. The filename_pattern should be double-quoted. Examples for filename_pattern specification:

Example1: For a 1D image series containing mcnor_5-8-06_arc_bk2_26_ca3_2_7.lsm and 
          mcnor_5-8-06_arc_bk2_26_ca3_2_10.lsm, the filename_pattern is
          "mcnor_5-8-06_arc_bk2_26_ca3_2_([0-9]*).lsm"

Example2: For a 2D image series containing Slide61Lbox003F_ChS1-T2.tiff and Slide61Lbox001A_ChS1-T2.tiff, 
          the filename_pattern is "Slide61Lbox00([0-9])([A-Z])_ChS1-T2.tiff"