TREES

download the TREES toolbox (interim version) for more recent Matlab versions:
Note: TREES 2.0 is coming soon; this is an interim version that is not entirely backward compatible, contains some bugs and does not yet contain the new features of TREES 2.0. However, recent Matlab versions are incompatible with version 1.15 and require the changes made in this package.Please contact bugtracker@treestoolbox.org to receive support on issues with the interim version of TREES toolbox.

[download zipped TREES interim]

download the TREES toolbox (v1.15) for Matlab:

[download zipped TREES 1.15]

download T2N (extension to interface Neuron):

from Bitbucket

from here

our new extended swc format (.nmf), Torben-Nielsen et al (SfN 2016 poster)
load_tree nmf_tree.

requirements Tested most thoroughly on the more recent Matlab versions (Matlab 2018a, 2017b, 2015b for v.1.15 and 2010a for first version) under Windows, Mac and Linux. Some functions for the reconstruction of neuronal trees from image stacks require the "image processing toolbox" of Matlab.
For semi-automated reconstruction we recommend following minimal hardware:
-    a lot of RAM, e.g. 8 Gbytes
-    64 bit
-    a mouse wheel
The original version of TREES toolbox was developed on a DELL precision T5400 with 8 cores (2 x Xeon X5450 3 Ghz 4 cores), 8 Gbytes of RAM and a NVIDIA Quadro FX 4600 graphic card, running 64-bit Microsoft Windows 7.

getting started Simply download TREES.zip (v1.15), unzip it in your favourite directory and open Matlab. Enter the TREES directory and type in:

>> start_trees

for more details have a look at the manual.

contact please send emails concerning questions, bug-fixes and extensions including example code only to the following addresses: info@treestoolbox.org and bugtracker@treestoolbox.org

license the TREES toolbox is published under the GNU General Public License Version 3 (GPLv3)

disclaimer Please note that this is a beta version and that we are aware that many bugs will be uncovered after making the TREES toolbox public. Unfortunately we do not possess the capacities to respond to all requests and questions sent to us. Please note also that subsequent releases will not be backward compatible.

Creative Commons License
This work is licensed under a Creative Commons Attribution-Noncommercial-Share Alike 3.0 License
last updated on 20 June 2018, Hermann Cuntz