I’m having a few problems with the MeasureObjectNeighbors module on CellProfiler.
If I have separately identified two distinct sets of objects from different images of equal dimensions - let’s say Objects1 and Objects2 - how can I ExportToSpreadsheet a full list of all the pairwise neighbourings between objects within a specified pixel distance (e.g. 10 pixels)? -
This should include:
Objects1 - Objects1 pairwise neighbourings
Objects1 - Objects 2 pairwise neighbourings
Objects2 - Objects 1 pairwise neighbourings
Objects2 - Objects2 pairwise neighbourings
where the first column represents the object we are finding the neighbours of and the second the neighbouring object.
I’ve had a play around with the ObjectRelationships ExportToSpreadsheet option.
I’ve also tried setting up four MeasureObjectNeighbors modules (for each of the 1-1 1-2 2-1 2-2 combinations above) followed by two separate ExportToSpreadsheet modules with the Neighbor and Location options selected for each of the Objects1 and Objects2 respectively.
I am getting errors trying both approaches (such as of the below form) and not getting the complete list of neighbourings I am hoping for (it seems to terminate early only outputting the Objects1-Objects1 neighbourings for example) -
Error while processing MeasureObjectNeighbors: (Worker) IndexError: boolean index did not match indexed array along dimension 1; dimension is 12335 but corresponding boolean dimension is 26833
Thanks for any assistance.