Different Directories

cellprofiler

#1

Hi! Happy new year!

New year, new questions :wink:

My data are spread over several different directories.
Is there a way to handle this?
Eventually I want to create batch files for running CP on a cluster…

Best wishes,
Christian.


#2

by the way: I am using WindowsXP.
best, Christian.


#3

Hi Christian,

The LoadImages module has the option of running the same analysis on images within subdirectories of any folder specified, by setting the “Analyze all subfolders” box. Currently, we have no way to combine images for the same analysis if they are in completely different folders (with no similar “top” folder), or drives, e.g. c:\images and d:\images.

To clear any confusion, you can organize your data such that they are located under the same top folder, even if they are in different subdirectories under this folder or not.

Regards,
-Mark


#4

hi Mark!

that’s what I suspected.
in principle I think this is a good way of doing things, its just that my amounts of data are so big that I cannot easily shuffle them around.

unfortunately, there seems to be no way to create symbolic directories within Windows such that it would also work with Unix.
its a real shame, because this would be a such a nice and clean solution! one could just put links to all directories in question into one top-folder!

well, i guess if i really need it i could fiddle around with LoadImages Module and see whether a “multiple directory feature” could be implemented…

anyway, thanks for the fast answer!

Best, Christian.


#5

Hi,

We’re definitely aware of this issue and we are working towards a more general image organization structure. Stay tuned!

In the meantime, is there any chance you can use CP on a Mac? Mac’s are definitely capable of creating UNIX-compliant symbolic links…
-Mark