[quote=“Fennell”]Having a lot of trouble getting any data out of the measure neurons module. Seems to be tracing the neurites fine but no neurite length or branching data. I keep getting this error if I try and run the neuron graph relationship.
Traceback (most recent call last):
File “cellprofiler\pipeline.pyc”, line 309, in run
File “cellprofiler\modules\measureneurons.pyc”, line 350, in run
File “cellprofiler\modules\measureneurons.pyc”, line 675, in make_neuron_graph
File “cellprofiler\cpmath\cpmorphology.pyc”, line 3648, in pairwise_permutations
File “scipy\sparse\csc.pyc”, line 147, in getitem
File “scipy\sparse\csr.pyc”, line 252, in getitem
File “scipy\sparse\csr.pyc”, line 190, in check_bounds
IndexError: index (203) out of range[/quote]
This error has been fixed, but you need to download a special compiled version, or use the Developer’s python code. See the comments here: viewtopic.php?f=14&t=1693&p=6687&hilit=MeasureNeurons#p6681
And re: extracting neurite length, that has yet to be added. However, a simple hack to get the overall length in the image you can take the skeletonized image, make a binary out of it using, say, ApplyThreshold, and then run MeasureImageIntensity on the binary. This is the next, and obvious measure, we will add. It is likely you can also get this info form the graph output, but we haven’t built a parsing tool for this yet, so you’d have to extract this info yourself for now.
Hope this helps,