Exporting the Image.xls file produced in batch mode


#1

Hi, I am a new CP user.
I need to work on a medium large set of images, so I tried the batch mode. BUt I don’t need to go in the database option.
I succefully created and ran my bacthes on a cluster (orchestra, in harvard medical).
Then I merged the all the *OUT.mat files together, and I created the total mergedOUT.mat file.
Finally, I exported the Nuclei and Cell values with the ExportData tool from the CP DataTool. Everything was OK.
Furtherly, from the total mergedOUT.mat file I tried to export the image values, with the ExportData tool, but this time it appears an error dialog window:

In an assignment A(:slight_smile: = B, the number of elements in A and B
must be the same.

Stack:
CPwritemeasurements in C:\Dokumente und Einstellungen\luca\Eigene Dateien\software\CellProfiler\CellProfiler_1.0.5122_XP32\CellProfiler_1.0.5122_XP32\CellProfiler_mcr\CPsubfunctions\CPwritemeasurements.m (324)
ExportData in C:\Dokumente und Einstellungen\luca\Eigene Dateien\software\CellProfiler\CellProfiler_1.0.5122_XP32\CellProfiler_1.0.5122_XP32\CellProfiler_mcr\DataTools\ExportData.m (99)
<<<<<<<<<<<<<<<<<<<<<

and in the output directory, appears an Merged_image.xls file totally empty.
I tried also to export images, using ExportData tool, from the same pipeline but without the batch module.
Running all the cycles on my PC, the exportdata for images worked well, producing the correct xls file.
Do I miss some command in exporting image data produced in batch mode, thorugh ExportData tool?
Thanks a lot
Luca


#2

Hi Luca,

It sounds like you are doing everything correctly. However, the current version (5122) of ExportData has a bug when at least one cycle has zero objects defined. See this post for more details: ExportData chokes on fields with zero identified objects

The next release of CP will fix this issue. In the meantime, you could try the suggestions in the post linked above, or identify the cycle with zero objects and remove it or change your settings to identify >=1 object.

Hope this helps (and apologies for the long response time),
David