What is the Toolbox
This Matlab toolbox is for reading/writing basic Vaa3D data file formats (image files .RAW, .TIFF, marker file .marker, point cloud file .apo, neuron file .swc which can indeed be used to describe any complicated graph) in Matlab. This is useful for post-analysis of the the image analysis and measurements.
Get the Toolbox
The toolbox is available as a sub-folder after you check out Vaa3D's source code. You can also directly check it out from the subfolder
What Are Included
This toolbox contains Matlab routines to read and write files with some formats defined/supported by Vaa3D.
Since some of the functions are mex functions, you may need to run the following command in Matlab to generate the mex function for your machine (assuming you have mex compiling setup in your Matlab):
The key Matlab routines included in this toolbox are:
|load_v3d_raw_img_file||load the .raw, .tiff image stacks used in Vaa3D (depending on file extension, the program automatically determine the file type)|
|save_v3d_raw_img_file||save the .raw, .tiff image stacks used in Vaa3D (depending on file extension, the program automatically determine the file type)|
|load_v3d_marker_file||load the .marker file|
|save_v3d_marker_file||save the .marker file|
|load_v3d_apo_file||load the .apo files (point cloud files)|
|save_v3d_apo_file||save the .apo files (point cloud files)|
|load_v3d_pointcloud_file||load the point cloud files used in Vaa3D (an overloading function provided for convenience)|
|save_v3d_pointcloud_file||save the point cloud files used in Vaa3D (an overloading function provided for convenience)|
|load_v3d_swc_file||load the .swc file (for neurons or other graphs)|
|load_v3d_neuron_file||load the neuron files in the .swc format (an overloading function provided for convenience)|
|save_v3d_swc_file||save the .swc file (for neurons or other graphs)|
Issue with the Matlab libTiff library & Solution
To use this toolbox to read/write TIFF files, the libtiff library will be needed in your Matlab search path. However, as Matlab uses an old version of libtiff, it is recommended to by-pass or update the default Matlab libtiff library file.
Let's use the Mac/Linux version(s) of Matlab as the example. What you can do is to disable the default libtiff in Matlab, and instead make it point to the good libtiff of the correct version.
Assume you have already installed libtiff under /usr/local/lib (if you have not built libtiff separately, but have built Vaa3D system using the build.macx or build.linux scripts, then you can also find the libtiff under the folder
The libtiff header files can be found under the folder
Note, if you cannot compile this toolbox using makeosmex function, then you may need to copy the several of these standard libtiff header files into this toolbox folder, so to make tiffio.h etc visible.
Then what you can do is to go to /Path-to-matlab/bin/maci (or maci64 or similar folder for a linux system), and list all libtiff files. And then rename or remove the original "libtiff.3.dylib" file. Then you can create a symbolic link to the correct one in the /usr/local/lib folder.
Then it should work (w/o need to re-start Matlab).