Dear all,
I'm trying to draw "average neurite labeling", that is make a line
selection along a neurite on a cultured neuron, and straighten it
using the Straighten plugin by E. Kocsis
(
http://rsb.info.nih.gov/ij/plugins/straighten.html), then averaging
all neurites to extract the informaation out of neurites of variable
shape. The straighten is a heavy, non-modal, archaic plugin that
obliges to draw the line selection inside the plugin window, one image
at a time. I've decided to dive into Java and make my first plugin (I
only know macros for now) : implement the Straighten algorithm in the
form of a simple plugin that you would call when a line selection is
active (with a window width parameter) and will return a new image
that has the length of the line and the specified width, containing
the straightened object calculated by the Kocsis algorithm. So I could
use all the nice ImageJ functions like ROI manager, stacks, macro
triggering of the straightening, etc...
Before I try something impossible, could someone skilled in java have
a look at the Straighten plugin (I uploaded the source here :
http://ftp.espci.fr/incoming/christo/Straighten_.java from the above
link) and tell me if it seems feasible to extract the algorithm part
from it to build the new, simpler plugin ? I've asked last year if
someone already tried to do precisely that or was willing to try, but
without luck, so I'll go the DIY way but I'll surely need some help.
Then, I think I'll try to integrate that with a semi-automatic neurite
tracing tool such as NeuronJ
(
http://www.imagescience.org/meijering/software/neuronj/, but source
is not available anymore) or the promising "Simple Neurite Tracer" by
Mark Longair (
http://homepages.inf.ed.ac.uk/s9808248/imagej/tracer/).
Christophe
Locked
