SNT discrepancy between Quick Measurement and Measure

I have been trying to use the new SNT (I always used Simple Neurite Tracer with no problems). My aim is to calculate dendritic length and perform Sholl analysis. I ahev come up against some problems. The first is that if I trace and then perform ‘Quick Measurements’ and then close the table and perform ‘Measure’, the 2 lines in the table have different values for ‘Cable Length’ which seems to be the value for total path/dendritic length. Most columns are the same, (but ‘Height’ value is also different, and ‘No tips’. I am performing this on all the paths.

The second problem is that when I import the traces file in (rather than just continuing immediately after tracing) and then try to perform either ‘Quick Measurements’ or ‘Measure’ it says ‘Multiple Rooted Structures exist’ (which they don’t according to this Path Analysis) and then errors if I select one and continue.

Thanks for any help
Emily

Welcome to the forum @ebrookes!

On “Quick measurements” vs “Measure” discrepancy: I cannot reproduce that issue upfront. The two menu entries call the same Command internally, so it is unlikely that the discrepancy is on the computation of the metric itself. However they could be measuring different things: “Quick Measurements” just does two things 1) chooses the most common options in the “Measure…” dialog, and 2) runs the “Measure” without prompt… Could it be that you have dendrites with different compartment tags and when you run Measure, you e.g., select the “distinguish compartments” option? If that is not the case, then I am a bit at loss.

On the second issue: On the most recent releases, If ‘Multiple Rooted Structures exist’, then you should be able to choose one (or all) for analysis. Maybe you are running an outdated version of SNT? Unfortunately with imagej.net down, I don’t think you will be able to run the updater smoothly. You will probably have to wait a couple of days until everything is restored.