I made a pipeline on CP 1.0.5122. It was working well.
I’d like to upgrade to 5811 so I installed the last release (bugfix branch).
Some modules changed, in particular FilterByObjectMeasurement. In this one, a new parameter was added:
For TEXTURE, RADIAL DISTRIBUTION, OR NEIGHBORS features, what previously measured size scale (TEXTURE
OR NEIGHBORS) or previously used number of bins (RADIALDISTRIBUTION) do you want to use?
The problem I got happens when I use MeasureObjectNeighbors module just before. I consider neigbors when 2 nuclei if
they are within a distance of 3 pixels. Then, when I want to filter nuclei that have at least 1 neighbor, it fails raising the
following error :
There was a problem running the anlysis module FilterByObjectMeasurement module which is number 35.
Attempted to access FieldnumsCategory(1); index out of bounds becasue numel(FieldnumsCategory)=0.
Image processing was canceled in the FilterByObjectMeasurement module (#35) because an error ocurred
when retrieving the data. Likely the category of measurement you chose, Neighbors, was not available for
Nuclei with feature 1possibly specific to image 'RescaledGreen' and/or Texture Scale = 3.
[size=85]error raised at line 123, FilterByObjectMeasurement[/size]
NB: ‘RescaledGreen’ is the image name I gave to FilterByObjectMeasurement parameter #5
(It is supposed to only affect the display).
I think it tries to get Neighbors_NumberOfNeighbors_RescaledGreen_3 value but I’m not sure
this is created in MeasureObjectNeighbors.
I have no idea of the reason of that error. Can somebody help me on that ?