I would like to use the data from the injections in the mouse brain connectivity tool, but I am having a slight issue understanding it.
When viewing the data, I have the option to switch the data from “Projection Volume” (in mm3) to “Projection Density.”
I am having an issue determining what “Projection Density” really means. Would anyone be able to provide a description and units for that?
Reviving this thread, as the first link seems to now be broken —
I see that the API defines Projection Density as “the proportion of projecting pixels in a grid voxel in [0,1]”
Yet the “projecting pixels” is not well-defined – is there anywhere where fluorescence is found?
The paper seems to go back and forth on this:
“It should be noted that passing fibers and terminals are distinguished with these methods.”
Yet, “All detected pixels are combined in the end to produce a combined classification mask (Fig. 12b).”
Finally “Although passing fibers can generally be distinguished from terminal zones by visual inspection of morphology in the 2D images (axon in terminal zones ramify and contain synaptic boutons), it is difficult to confidently make this distinction algorithmically. While major fiber tracts annotated in the atlas are masked out, a different experimental design is needed, for example the use of synaptophysin as a molecular label, to truly isolate synapses in terminal zones.”
So is the correct interpretation that major axon tracts are filtered out, but many other passing axons may be included in “projecting pixels”? Or can no such guarantees be made at this point?