rona baron <
[hidden email]> wrote:
>
> Hi,
>
>
> I used the 'simple neurite tracer' plugin to trace some processes of a
> neuron.
> Since I'm new in this field, does anyone know if I can measure the volume of
> the processes that I measured?
>
> thanks,
> Rona
Rona,
If you run "Help > Update Fiji", you should get the latest
version of Simple Neurite Tracer, which can give you volume
measurements in two ways.
1. If you using the "Fill Out" option to create a fill around
a path and then click "Export as CSV" in the Fill Window,
there should be a column in that file with the volume at
that particular threshold. As a word of warning, since the
structures one traces tend to be long and thin, very small
adjustments in the threshold can have a large effect on the
volume measurement. So, if you're wanting to compare
volumes across multiple paths or multiple images, it would
be a good idea to (a) use exactly same threshold for each
and (b) apply some normalization to the images beforehand
particularly if they have a lot of variation in contrast /
brightness.
2. Paths which have had midlines and radii fitted with the
"Fit Volume" option now will have a value in the column
"ApproximateFittedVolume" in the CSV output that you get
from "Export as CSV" in the main dialog. Since the
behaviour of this fitting can be rather unpredictable, I
wouldn't recommed using this value (hence the
"Approximate" bit)...
I hope that's of some use.
regards,
mark
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