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Software tools - installation

Requirements


Obviously, ImageJ (or Fiji) is required. If you want to be able to compile the plugins yourself, make sure to install the version bundled with Java, if you do not already have a Java Development Kit installed on your machine.

To run the second component of the tool and if you are on Windows, you can use the pre-built binaries provided here, in which case you probably need nothing else. Otherwise, you will at least need the Python language interpreter (version 2.5+, but not 3.x), as well as the user interface library wxPython; in addition, if you want to save the output in Excel format rather than plain text, you will need the pyExcelerator module.

Update April 17, 2018: I have started to convert the Python components, beginning with DistToPath, to Python 3. Thus, for converted tools, Python 3 instead of Python 2 is required if you use the source distribution. These tools also use the openpyxl package instead of pyExcelerator. In Python 3, wxPython and openpyxl packages are installed from the command line using the command pip install [package], where [package] is the package to install.

 

Installation instructions


Updated August 20, 2019. Locate the installation folder of ImageJ or Fiji. If you have the zip file with the compiled plugin (which is recommended), unpack the zip file the new folder and place the jar file in the plugins folder. Start (or restart) ImageJ/Fiji. The plugin should appear in the Plugins menu. If you have the java source of the plugin, unpack the folder in the compressed file and use Maven to compile the source. The Plugins/Compile and Run... command does no longer work. Copy the jar file (not the file ending in .sources.jar) in the target subfolder to the plugins folder of the ImageJ installation folder and restart ImageJ.

The second component of the tool can be unpacked to any folder and run from there. If you have the pre-built version for Windows, just double-click [tool].exe where [tool] is the name of the tool (e.g., PointDensity.exe). If you have the Python source files, run [tool].py or [tool].pyw. You may have to run the .py file from the command line by typing python [tool].py. If the Python interpreter is not found, check your Python installation (you may have to specify the path to the python interpreter). If nothing happens or if a window briefly appears and then disappears, run the component from the command line to see possible errors. If you receive the following error:

Traceback (most recent call last):
File "PointDensity.py", line 4, in <module>
import wx
ImportError: No module named wx

make sure you have installed wxPython. If some other error occur, please e-mail me.

 

License information


All tools are released under the MIT license, which essentially means that you can freely modify and redistribute the tools, provided that the modified tools include the original copyright notice and license text.

 


Page manager: max.larsson@liu.se
Last updated: 2019-08-20