FillObjects plugin


#1

Hi,
I have been trying to use the FillObjects module (https://github.com/AetherUnbound/CellProfiler/blob/dd2175d19fc92e12f6451b45bcd4249b1e55fa87/cellprofiler/modules/fillobjects.py) on my 3D watershed objects. I get the following warnings within a few seconds:

C:\Users\uqjkesby\AppData\Local\Temp_M5589~1\skimage\util\dtype.py:118: UserWarning: Possible sign loss when converting negative image of type float64 to positive image of type bool.
C:\Users\uqjkesby\AppData\Local\Temp_M5589~1\skimage\util\dtype.py:122: UserWarning: Possible precision loss when converting from float64 to bool
C:\Users\uqjkesby\AppData\Local\Temp_M5589~1\skimage\morphology\misc.py:122: UserWarning: Only one label was provided to remove_small_objects. Did you mean to use a boolean array?

It then just seems to get stuck (using ~15% CPU with allocated memory shifting between 5-8 GB). Watershed takes about 5 mins and I left this for over 5 h with nothing changing. Any thoughts?

Also, a minor thing, the options in this module have a ‘minimum hole size’ but the help says that this is the maximum hole size to be filled.

Thanks in advance,
James


#2

Update: it did finish when run overnight. Seems this module just takes a lot longer than I expected.