...before your download
VANO is free, but you will have
to agree the license terms on this page, before downloading, using, running, editing, or changing any portion of codes in this
package. The download link is at the end of the license terms. Downloading the package below means you have read and agreed on the License and Agreement terms. If you do NOT agree, please do NOT proceed to download.
Latest Versions
Note: VANO was previously called "WANO" (Worm AnNOtation), due to historical reason. For compatibility issues with existing users, the following installable versions still bear the name "WANO". But this name will all be changed to VANO in future releases. Pre-compiled versions (32/64bit):
64bit version:
- You can download the 64bit for Mac Snow Leopard from the link above.
- To produce the 64bit VANO is quite easy if you have a GNU c++ complier, you can download the source code below and run the same batch compiling command. The only "special" requirement is that your QT installation should be of course 64bit as well. Also the libtiff library should be compiled as 64bit.
Source codes and build instructions for all platforms (Mac, Windows, and Linux):- You can (and are encouraged to) checkout the latest version (1.82) from the following SVN site:
- svn co https://svn.janelia.org/penglab/projects/vano/trunk vano
- Build instructions:
- Mac
- 32bit: run the following commands in the c++ folder of the project (assume you already have QT, g++, and make, and libtiff compiled at /usr/local/lib folder):
- qmake vano.pro
- make
- (then you can run vano.app)
- 64bit: run the following commands in the c++ folder of the project
(assume you already have 64bit QT, g++, and make, and libtiff compiled at
/usr/local/lib folder):
- qmake CONFIG+=x86_64 vano.pro
- make
- (then you can run vano.app)
- Linux
- 32/64bit: run the following commands in
the c++ folder of the project (assume you already have QT, g++, and
make, and libtiff compiled at /usr/local/lib folder):
- qmake
vano.pro
- make
- (then you can run vano)
- Windows
- 32bit, MinGW complier: run the following commands in
the c++ folder of the project (assume you already have QT, and libtiff compiled):
- qmake
vano.pro
- make (or mingw32-make)
- (then you can run vano.exe)
- 32/64bit, Microsoft Visual Studio: launch the 32bit or 64bit MSVC compiler terminal (you can find in MSVC menu folders), and run the following commands in
the c++ folder of the project (assume you already have QT, and libtiff compiled at /usr/local/lib folder):
- qmake
vano_msvc.pro
- nmake -f Makefile.Release
- (then you can run vano.exe)
- Previous version. v1.741 : (30M bytes). Assume you have Qt set up and libtiff installed, you can simply run vano_build.??? script (i.e. vano_build.macx for Mac, and vano_build.bat or vano_build.msys for Windows) to compile. For Windows, you can use the MinGW compiler. If you don't know how to do this and really want to compile, please contact Hanchuan Peng.
All old versions have been removed. If you have a problem to run, or have other questions, please feel free to contact me.
Other Software That Can Read/Write VANO Files
A VANO data set normally consists of 4 files. You can find examples of these files in the "Example Data" page. The following summarizes what are they and how to read/write them. Note that this Matlab Toolbox for V3D data file IO can be used to read/write the 3D images and point cloud .apo files as well.
- linker file (.ano file): a simple text file indicates where are the other three files, so VANO can open them. You can use any plain text editor (e.g. vi) to generate/edit this file. If some links in this file is broken, VANO will automatically open a linker fixer dialog so that a user can easily select files to fix the broken link(s). One example of an .ano file can look like the following.
GRAYIMG=file1.tif
MASKIMG=file2.raw
ANOFILE=file1.apo
- subject image: a 3D tif or lsm image stack, or Hanchuan Peng’s raw file (with a simple header indicating size, endian, etc). This is indicated by the “GRAYIMG” keyword in a linker file). You can use any software that can produce 3D TIFF stacks to generate this file, e.g. V3D, Matlab, ImageJ, etc. You can use V3D to produce the customary RAW file as well.
- mask image: normally a .tif or .raw file, or anything following the “MASKIMG” keyword in a linker file. This is an image stack has the same dimensions with the original image stack, but contain the segmented image regions, each with a distinct label (i.e. intensity value). You can use V3D to generate the RAW file (using V3D cell segmentation functions) or convert a TIFF stack to the customary RAW file.
- annotation file (.apo file, or anything following the “ANOFILE” keyword in a linker file): a simple 17-column CSV file (comma separated values) in plain text format, which records all the users’ annotations about the image objects, as well as the quantitative statistics information of image objects in the subject image stack computed based on respective regions defined in the segmentation mask image. You can use any plain text editors to read/write the file (of course, you need to ensure the same set of columns should be used, just like the Example Data). You can also see the point cloud rendering of the annotation file in 3D using V3D software.
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