[Gusdev-rad-issues] GenePixElementResult

[Josef J. <ju...@cs...>]

In looking over the several typical output files of GenePix,
I see that most of the important values of these files map
to fields of the RAD.GenePixElementResult view:

     GenePix                  RAD table

     X                      ?
     Y                      ?
     Dia.                   RAD.GenePixElementResult.SPOT_DIAMETER
     F635 Median            RAD.GenePixElementResult.FOREGROUND_MEDIAN
     F635 Mean              RAD.GenePixElementResult.FOREGROUND_MEAN
     F635 SD                RAD.GenePixElementResult.FOREGROUND_SD
     B635 Median            RAD.GenePixElementResult.BACKGROUND_MEDIAN
     B635 Mean              RAD.GenePixElementResult.BACKGROUND_MEAN
     B635 SD                RAD.GenePixElementResult.BACKGROUND_SD
     % > B635+1SD           RAD.GenePixElementResult.PERCENT_OVER_BG_PLUS_ONE_SD
     % > B635+2SD           RAD.GenePixElementResult.PERCENT_OVER_BG_PLUS_TWO_SDS
     F635 % Sat.            RAD.GenePixElementResult.PERCENT_FOREGROUND_SATURATED
     ...                    ...
     F Pixels               RAD.GenePixElementResult.NUM_FOREGROUND_PIXELS
     B Pixels               RAD.GenePixElementResult.NUM_BACKGROUND_PIXELS
     Circularity            RAD.GenePixElementResult.CIRCULARITY


however as far as I can tell, there is no place in the view to put
the values of the columns that are labeled "X" and "Y" from a GenePix
output file.  GenePix describes these values as follows

    X     the X-coordinate in µm of the center of the feature-indicator associated with
          the feature, where (0,0) is the top left of the image.

    Y     the Y-coordinate in µm of the center of the feature-indicator associated with
          the feature, where (0,0) is the top left of the image.

This is important information that we do not want to toss away.
Is this an oversight, or have I missed something?

I hope columns for these two values can be added to this table/view.
We will have to go a head an this columns in our locally installed
version of RAD anyways, as we need this.

Thanks Josef




Josef Jurek

Daphne Preuss Laboratory
Molecular Genetics and Cell Biology
The University of Chicago
ju...@cs...

voice: (773) 834-3985
fax:   (773) 702-6648