Instead of selecting each spot interactively, you can use a list of spots from a disk file to make up to 10,000 densitometric measurements automatically. These are plain text files that can be produced by tnimage or created manually. It is often convenient to identify the spots automatically, save the results in a file, then perform densitometry on the spots all at once.
Below is the file format for spot lists:
#Unwarped spot list #Label orig.x orig.y Size Signal xmin ymin xmax ymax Identity 1 430 75 374 1103 424 74 450 108 spot1 2 604 91 32 39 603 90 610 99 2nd_spot 3 466 93 70 112 463 92 471 109 aldolase_A 4 422 101 66 94 411 100 427 114 4
Any line not containing data must start with a `#'. The file must have at least 10 columns, separated by white space. The first column is a text label identifying the spot. This label cannot contain white space. The other columns are the center x and y position of the spot (measured in pixels from the upper left corner of the image), the spot's size and total signal, and the bounding box (xmin, ymin) to (xmax, ymax) of the spot. The Size and Signal columns are ignored in densitometry and may be set to 0. The last column is a second optional label containing the `identity' of the spot.
This file format is produced by tnimage's grain counting and image registration functions.
When a warped or unwarped spot list is created during image registration, the list is stored in memory and can also be accessed in spot densitometry by clicking ``Data Source.. Spot list''.
It is recommended to use ``Auto background (fuzzy k means)'' when performing densitometry on lists in case the background is uneven. Currently only densitometry of rectangular areas is supported for lists.