The data points are stored in plain text files
in the same format as the grain counting files produced by imal.
The five-line grain counting header is optional, and is ignored if
present. Lines starting with a # are ignored.
Data points are stored one per line as shown below, in the order:
label 
tab
x-coordinate tab y-coordinate tab value.
The label can be any string, but cannot contain white space.
The x and y coordinates are distances in pixels from the upper left
corner of the image. The data points do not have to be in any particular
sequence.
All lines containing non-data must start with a #.
File format for single sets of data points
There are two data files: one for the reference image, containing the coordinates and labels of all the known spots, and one for the unknown image, containing all the data points to be remapped. The first 9 columns of each file are used. Columns are separated by white space. If a column is empty, values are set to 0. Columns cannot be skipped. A complete table is shown below. The columns for minx, miny, maxx, and maxy are used for densitometry. If the minx, miny, maxx, and maxy columns are omitted, imal asks for a spot size. Enter the width in pixels for the spots. In this case, all the spots will be assumed to be the same size.
Example data file with 5 columns
# Size analysis of /home/tjnelson/data/30a/30a38a-filtered5.tif # Largest signal 2793 # Most frequent size 23 (count=7) # Largest object 457 # Label x pos y pos Size Signal # All the above lines are ignored calcineurin 566 149 149 422 trypsin 618 176 325 1018 S6_kinase 575 194 86 139 36 698 209 373 1015 49 694 238 413 1468
Example data file with 9 columns The additional columns are produced by imal's grain counting and are essential if the results are to be used for densitometry (The minima and maxima are the bounding box of the spot). Any calibration data is included in columns 10-12.
# Obj. x pos y pos Size Signal Min.x Min.y Max.x Max.y 1 158 6 18.02 20.10 155 5 162 12 2 152 13 5.12 5.4 151 12 156 15 3 262 18 11 11.5 260 17 265 23
In the above example, spot ``1'' is centered at (158, 6), and fits in a bounding box between (155,5) and (162, 12).
File format for 2 sets of data points (a.k.a. match table) (Created by ``Save match table'') These files contain the two original data sets. If you clicked ``correlate points'', the Unknown data set will be permuted so that identified corresponding points are on the same line. Any unmatched data points are listed at the end.
#Ref Ref.x Ref.y Unk Unk.x Unk.y xmin1 ymin1 xmax1 ymax1 xmin2 1 158 6 1 158 6 155 5 162 12 155 2 152 13 2 152 13 151 12 156 15 151 3 262 18 3 262 18 260 17 265 23 260 4 276 18 4 276 18 275 17 278 21 275 5 238 22 5 238 22 234 21 243 30 234 #Unmatched reference points 11 272 133 None 0 0 259 132 297 158 0 # Unmatched unknown points None 0 0 3 1170 101 0 0 0 0 1167
(continued)
ymin2 xmax2 ymax2 Score
5 162 12 20
12 156 15 5
17 265 23 11
17 278 21 3
21 243 30 35
0 0 0 0
100 1178 114 0
Unwarped Spot list and Warped spot list - contains spot name, spot x, spot y, xmin, ymin, xmax, and ymax of each spot after remapping (Created by ``Create warped spot list'' or ``Create unwarped spot list''). This format is the same as the original data files with the addition of an extra column for Identity. This means files of both types can also be used for spot densitometry. The unwarped spot list shows the spots in their original locations, along with their identification. This would be the appropriate file to create if you did not warp the image. The warped spot list shows the spots in their new locations after warping. This would be the appropriate file if you warped the image.
# Unwarped spot list #Label orig.x orig.y Size Signal xmin ymin xmax ymax Identity 1 398 97 374 1103 395 96 402 103 9 spot_21 1905 117 32 39 1888 98 1905 117 cytochrome_C spot_22 1509 153 70 112 1491 134 1509 153 actin 25 1817 157 123 177 1802 139 1817 157 protein-44 27 679 185 133 269 659 165 679 185 1234
This means spot ``spot_21'' is centered at (1905, 117), is bounded by a rectangle from (1888, 98) to (1905, 117), and was calculated to be the same as the cytochrome_C spot in the reference image.
Landmark list containing corresponding points and locations This file shows the label and x and y coordinates of each known landmark and of its counterpart in the unknown image. The file has to be created manually from the data point files. If the point correspondences are unknown, clicking ``Correlate points'' will rearrange the right 3 columns to put matching points on the same line.
#ref ref x ref y unk unk x unk y 20 494 145 40 461 116 28 503 185 49 468 152 29 486 189 53 452 163 46 430 227 65 376 196 42 462 221 67 418 198 49 694 238 68 653 200
In the above example, spot ``20'' on the reference image is centered at (494, 145), and corresponds to spot ``40'', which is centered at (461, 116) on the unknown image.