At http://www.3dbar.org/wiki/barSoftwareInstallation you can find installation
instructions. Please make sure you install packages related to your Ubuntu
version. Please disregard 'Getting code' section and use provided code instead.


Once the software is installed, you need to generate CAF representations
of data of interest. For this you need to use parsers. We provide here
the following parsers:


1.  ScalableBrainAtlas DB08 template
    (http://scalablebrainatlas.incf.org/main/coronal3d.php?template=DB08)

2.  ScalableBrainAtlas PHT00 template
    (http://scalablebrainatlas.incf.org/main/coronal3d.php?template=PHT00)

3.  ScalableBrainAtlas WHS09 template
    (http://scalablebrainatlas.incf.org/main/coronal3d.php?template=WHS09)

4.  ScalableBrainAtlas WHS10 template
    (http://scalablebrainatlas.incf.org/main/coronal3d.php?template=WHS10)

5.  ScalableBrainAtlas LPBA40_on_SRI24 template
    (http://scalablebrainatlas.incf.org/main/coronal3d.php?template=LPBA40_on_SRI24)

6.  ScalableBrainAtlas RM_on_F99 template
    (http://scalablebrainatlas.incf.org/main/coronal3d.php?template=RM_on_F99)

7.  the Waxholm Space Atlas (the source mouse brain volumetric dataset)

8.  the Waxholm Space Atlas (the source mouse brain volumetric dataset), another
    delineation
    (http://software.incf.org/software/waxholm-space/waxholm-space/LabeledAtlas0.5.1/file_download?file_field=file)

9.  Paxinos and Watson "The Rat Brain in Stereotaxic Coordinates" PDF atlas.

10. Franklin and Paxinos "The Mouse Brain in Stereotaxic Coordinates" PDF atlas.

11. The Allen Mouse Brain Atlas
    (http://mouse.brain-map.org/atlas/index.html)


To generate CAF dataset for data from ScalableBrainAtlas DB08 template execute
the following commands in the root directory of the software:

# source setbarenv.sh
# make sba_DB08

The first line sets the path to the API and uses appropriate parser to download
the data from SBA and do the transformation into the CAF dataset.

You can also generate that way CAF dataset for any of following SBA templates:
"PHT00", "WHS09", "WHS10", "LPBA40_on_SRI24" and "RM_on_F99" just by replacing
"DB08" with the name of the source template.

In order to generate that way CAF dataset for the Waxholm Space Atlas replace
"sba_DB08" with "whs_0.5" or "whs_0.51" (for another WHS delineation).

To generate CAF dataset from Paxinos and Watson atlas you have to supply
the parser with PDF file delivered with printed copy of the atlas.
Execute the following command in the root directory of the software:

# bash bin/parsers/paxinos_watson_rbisc/make_svg_from_pdf_rat.sh <PDF path>

You have to replace "<PDF path>" with a valid path to the file mantioned above.
The CAF dataset will be stored in the 'atlases/paxinos_watson_rbisc/caf-src'
directory.

If the result of parsing does not satisfy you, you can edit slides ripped
from the PDF atlass manually with your favourite SVG editor.

The slides are located in 'atlases/paxinos_watson_rbisc/caf-src' directory
and named 'N_pretrace_v1.svg' where N is the slide number.

Once you have your slides edited execute in the root directory of the software:

# make -f make_pw_rbisc.mk

to reparse the edited slides.

Similarly for Paxinos and Frnklin atlas you have to execute:

# bash bin/parsers/paxinos_franklin_mbisc/make_svg_from_pdf_mouse.sh <PDF path>

in the root directory of the software. The CAF dataset will be stored in
the 'atlases/paxinos_franklin_mbisc/caf-src' directory.

To reparse the edited slides execute:

# make -f make_pf_mbisc.mk

in the root directory of the software.

Generation of CAF dataset for The Allen Mouse Brain Atlas might be a little
more complicated unless you have installed the Advanced Normalization Tools
(ANTS; http://picsl.upenn.edu/ANTS/). ANTS have to be availiable as shell
commands (for an example by adding ANTS 'bin' directory to environment value
PATH).

To generate CAF dataset from The Allen Mouse Brain Atlas execute:

# source setbarenv.sh
# make aba

in the root directory of the software.


Once you have a CAF
of any dataset you can test the GUI for structure creation. To do it, in
the main directory run:

# ./3dbar.sh

and choose in the menu Atlas/Open and select 'index.xml' file of chosen CAF
dataset.

To test, click the topmost label on the tree in the left panel and press
'Perform reconstruction' button in the right panel. The reconstruction process
will start. When it is finished, chose in the menu Edit/Save Model. It allows
you to put it later i context by right click on the ontology tree.


In order to generate documentation execute:

# make doc

The documentation for API can be viewed by opening 'doc/api/html/index.html'
and the documentation for 3dBAR graphic interface can be viewed by opening
'doc/gui/html/index.html'.

