I hope it's OK to post this here - a few people have suggested
that I should describe here some of the new features that have
been added to the Simple Neurite Tracer plugin for ImageJ, since
the last time I mentioned it on this list it was a long time
ago, and it was still very much of alpha quality then.
The plugin is now only distributed as part of Fiji:
http://pacific.mpi-cbg.de/wiki/index.php/Simple_Neurite_TracerIn addition to many bug fixes, some highlights of recent
development include:
* You can now trace entirely in the 3D Viewer's interface,
assuming the image stack hasn't got too much background.
There's an example session here:
http://www.youtube.com/watch?v=SrPeSwu31Zs ... and instructions here:
http://pacific.mpi-cbg.de/wiki/index.php/Simple_Neurite_Tracer:_3D_Interaction * Import and export of SWC files is supported. The importer
contains options for dealing with various common but
non-standard variants of the SWC format (e.g. those
distributed as part of the Diadem Challenge):
http://pacific.mpi-cbg.de/wiki/index.php/Simple_Neurite_Tracer:_"Export_to_SWC"_Tutorial
http://pacific.mpi-cbg.de/wiki/index.php/Diadem_Challenge_Data * There is a graphical interface for Sholl analysis in 2D and
3D:
http://pacific.mpi-cbg.de/wiki/index.php/Simple_Neurite_Tracer:_Sholl_analysis * You can preprocess your image with any filter, and force the
tracing to take place over those values:
http://pacific.mpi-cbg.de/wiki/index.php/Simple_Neurite_Tracer:_Preprocessing_Data_for_Better_Results * The user interface has been significantly simplified, with
more options now moved to pull down or pop-up menus.
* For visualization purposes, you can colour the paths
according to values in another image stack. (For example,
if you have a second channel which represents a synaptic
density marker, you can colour your traces according to the
density of synapses at each point along the path.)
* The support for placing points at high magnification has
been much improved.
http://pacific.mpi-cbg.de/wiki/index.php/Simple_Neurite_Tracer:_Accurate_point_placement * You can run the "Analyze Skeleton (2D/3D)" plugin on paths
traced in Simple Neurite Tracer via the '"Analysis > Run
Analyze Skeleton"' option.
* Selecting particular paths used to be awkward when many
paths had been traced - there are now easier ways to do
this:
http://pacific.mpi-cbg.de/wiki/index.php/Simple_Neurite_Tracer:_Selecting_paths * Measurements can be exported for loading into spreadsheets
or statistical software via the "Export to CSV" options.
* There is an intuitive way of choosing the scale of
structures of interest when using the Hessian-based
analysis, using the "Pick Sigma Visually" option.
* In the 3D viewer, paths can be displayed with surface
reconstructions, as lines or (where radii have been fitted
at each point) as lines and discs.
If you find any bugs or problems when using the plugin, please
let me know, either by email (off-list) or via Fiji's "Help >
Report a Bug" option. As ever, patches and other contributions
are very welcome.
best regards,
mark
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