Export to spreadsheet: truncating data?

I’ve been using CP on Mac OS 10.6.2 for a few days now to try to analyze Y2H spot data. I’ve been using the “yeast patch” example as a template pipeline and for the most part have things working.

The difficulty is in the “export to spreadsheet” module. If a grid is assigned, and the measurements taken on colonies in the grid, when exporting to a spreadsheet the data is truncated to the number of objects identified. For example, in a 48 position grid, if colonies are identified in 20 of the cells, only the first 20 rows are exported. The “0” cells are reported, and in the correct order, but the .csv is truncated after 20 rows. I went back to the yeast patch example and it exhibits the same behavior, the last 6 entries are missing as there are only 90 cells in the grid with colonies.

Measurements are taken, I can get them to export on the image of the plate, but the spreadsheet export is not behaving for me.

I’ve tried Export all measurements and using the data to export pulldown… no luck.

Is there something that I’m missing?

Best,
Evan

Pipeline:
LoadImages
Crop
ImageMath
CorrectIlluminationCalc
CorrectIlluminationApply
IDPrimaryObjects
DefineGrid
IDObjectsInGrid
MeasureObjectSizeShape
ExportToSpreadsheet

Hi,

Thanks for reporting this. From the symptoms, it appears to be a bug in ExportToSpreadsheet. I see the same behavior in ExampleYeastPatch. We will look into this further and report back.

Thanks,
David

Thanks!

While we fix the bug, you may be able to work around this by adding a ReassignObjectNumbers module to the pipeline after IdentifyObjectsInGrid with the “Unify” operation selected and a max distance of 0. This “packs” the object numbers, and I believe causes all the non-empty objects to be exported (but none of the zero-area objects).

The new beta fixes the bug for me, thanks!

Is there a way to export the zero area objects as well? For example, I lay a grid over a Y2H plate image, id primary objects(colonies), and for each cell I want either the size of the colony or a zero if no colony is detected.

Best
Evan

Re: exporting zero-area objects: Unfortunately, at this point, no. While investigating this issue, it brought up a bug in IdentifyObjsInGrid. Once this fix is released in the next version, you’ll be able to do this task.
-Mark

Thanks for the update!