I’m currently working on characterizing the physiology of Purkinje neurons form rat cerebellum (dissociated cell culture) when treated with different compounds.
I am using the simple neurite tracer plugin, and it is working very well for my purpose. What I need from the plugin is to count how many orders or dendrite segments there are for each neuron (viewed nicely in the hierarchy of the segments in the “all paths” window), as well as knowing how long the segments are. The goal is to determine if there is a difference in number of branching/orders of dendrites in control vs treated cultures (and if they get longer or shorter).
The problem arises when I save the data as a csv file, and import it to Excel where I make my graphs. It would take too much time figuring out which segment is of what order only looking at which other segments they are attached to (which is how the data is presented). To solve this, I have manually renamed the segments in the “all paths” window to follow a labelling code as follows:
Segment of primary order: a number (1 for primary) and a letter (to differentiate from other primary neurons) for example: 1a, 1b and so on.
Segment of higher orders: a number (2 for secondary - means it sprouts from a primary segment, 3 for tertiary, and so on), a letter (to identify which primary segment it belongs to) and another number (to see how many segments of this particular order that belong to the primary segment) for example: 2a01, 3a01, 3a02 (where 2a01 sprouts from 1a, and 3a01 and 3a02 sprout from 2a01).
When I save this and open it in Excel, I can sort the data by segment order, and easily use the data I need; but this is a quite time consuming method.
My question therefore is:
Is there any way I can automatize the labelling of the dendrite segments?