Invalid File Identifier for UnifyObject Module

cellprofiler

#1

I am receiving an error for an indivalid file identifier when I try to add the module, “UnifyObject” to a pipeline. If ‘fgetl’ is used rather than ‘fgets’, it may generate a valid file id, but I’m not sure how to edit the source code for this program.


#2

Actually, I can’t find the m-file for this module anywhere.


#3

Hi Ashley,

Have a look at this prior forum post: http://forum.image.sc/t/missing-module/17701/3. The UnifyObjects module was omitted from the previous compiled version, and is still under development. We’ll update you when it arrives.

Regards,
-Mark


#4

Thanks. In the mean time, any suggestions on how to identify non-circular objects? I’m attempting to identify and quantify the orientation of fibers (grayscale, but intensity is not constant). I was going to merge touching objects together, but maybe there is a better module? Is “soon” the next week? month? year?


#5

Hi Ashley,

The new release should be coming out within the next couple of weeks, with UnifyObjects. For identifying non-circular objects, you should be able to use IdentifyPrimAuto with the correct thresholding method- and perhaps selecting Try to merge small objects with nearby larger objects? Perhaps you could post an image of the fibers you are trying to identify and I could direct you as to which modules would be appropriate for the segmentation.

~kate


#6

Hi Ashley,

Just a quick follow-up: The new version of CellProfiler has been released and includes the UnifyObjects module. You can download it from here.
-Mark