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02/24/2009

 

Blob Tool | Blob Statistics | Preprocessing images before blobbing

Blob Batch Button

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The Batch Button is for obtaining particle statistics from a folder of images.

 

 

Most other functions for processing a folder of images are in the Process Folder Tool.  If a file named process-images.txt is put in a companion folder to the folder with the images (a folder named <image folder name>-lx) then Lispix will perform the processing steps in each line of this file, just as the Process Folder Tool would do, before each image is blobbed.

 

Batch Commands

These commands are for collecting measurements of particles in a folder of images.  This is done in two or three stages:  1) selecting thresholds for the images, 2) collecting the statistics for the images, and 3) making a summary spreadsheet file, if desired, for the statistics for each image.  This last file is used by the Fields in Circle Tool, to colorize a mosaic of fields by number of particles, greatest particle, etc.  The thresholds are saved in a tab delimited text file, one image per line (or row).  The blob statistics (particle measurements) are saved in a similar text file, one blob per line.  The summary statistics are saved in a text file, one image per line.  These text files are saved in a folder named <image folder name>-lx, which follows the folder of images in a directory listing, for example, if the images are in a folder called "Fields", then the directory structure looks like this:

The threshold files and statistics files are named by the thresholding method, such as "fixed-thresholds.txt" and "fixed-stats.txt" for the one-threhold-fits-all method, and "manual-thresholds.txt" and "manual-stats.txt" for the manually-chosen-threshold-for-each-image method. These text files can be edited with a text editor, and imported into a spreadsheet.  The blob stats and summary files are easier to read when imported into Excel.  The order of the images listed in the threshold file is not important.

  1. Making the Threshold File
  2. Making the Blob Statistics File
  3. Making the Blob Statistics Summary File.