LoadImages with same file name

Hello,

I’m new to CellProfiler and I have a question concerning LoadImages module. I’m acquiring my images with a BD Pathway and images are stored in the following configuration:

/2010-04-27_000/Well A01/Alexa 488 - n000000.tif
/2010-04-27_000/Well A02/Alexa 488 - n000000.tif
/2010-04-27_000/Well A03/Alexa 488 - n000000.tif
/2010-04-27_000/Well A04/Alexa 488 - n000000.tif

Every image has the same file name and is store in a different folder. I put the folder /2010-04-27_000 as “Default input folder” and used the “Analyze sub-folder” option to load my images and extract well metadata. However it seems that loading different images with same file name is causing problem for analyzing and saving images. I tried to use the RenameOrRenumberFiles module to rename my images with the “Add text to file name” option but I couldn’t add metadata in this field to give a different name to each image. Is there a solution within CellProfiler to this problem?

Thank you.
Julien

Hi Julien,

Could you give us more details on what sort of behavior you are observing during analysis/saving? Also, are your problems similar to what’s described here?

Regards,
-Mark

Hello,

In fact it was the same problem. Sorry for the poor search I ran in the forum…
The images were saved as stack of one pixel width or when I try IdentifyPrimaryObjects the software said it receives color images although I had gray level images. In my particular case, the problem was solved when I remove the file “Alexa 488.dye” from the default input folder. Unfortunately, the files are too big to be attached to the post.

Thank you!
Julien