Skip to content


Subversion checkout URL

You can clone with
Download ZIP
Java Python
Branch: master

Fetching latest commit…

Cannot retrieve the latest commit at this time

Failed to load latest commit information.

Microscope Communicator


Christian Tischer (ALMF, EMBL Heidelberg)

Kota Miura (CMCI, EMBL Heidelberg)

Antonio Politi (CBB, EMBL Heidelberg)


Please compile the source file using maven or download the jar file.

You need a library "Apache Commons IO" ( as well so please also download the jar file from the above mnentioned site and place the file also in the ImageJ or Fiji plugin folder.

Commands will be located under Plugins > ALMF >


Microscope Communicator (Outdated)

Select Microscope type, choose an action and a command to send.


Allows to write and read from registry a specifc key

Run a Macro on New Image

Select a folder to monitor appearance of new images (where captured images are saved). Upon appearance, A macro of your choice will be executed on that new file. Maximum interation could be set in the dialog as well.

The file path should be retrieved in the macro by

filepath = getArgument()

During monitoring, a small window will be staying on your desktop. To force quit the monitoring, click stop or close button.

Run a Jython on New Image

Similar to above, but runs Jython scripts.

The file path to the new image will be stored in a variable called


and can be used directly in the script. As a very short example, see the following code:

fullimagepath = newImagePath # argument passed from the Microscope Communicator
IJ.log("NewFile " + fullimagepath)

This Jython script is with only two lines. What it does when a new file is added to the folder being watched is that the script prints out the file name in the log window.

The trick is the variable newImagePath in the first line. This variable is generated by the plugin and is already an object when the plugin is running. It's a string object and holds the name of the image file that was added. More simply it could be just a line:

IJ.log("NewFile " + newImagePath)

This works as well.


1.1.2 (20130311)

Antonio's bugfix:

  • fixed restart button. Now it first deletes old monitor than startnewmonitor

1.1.1 (20130311)

Antonio's contributions:

  • pom.xml updated.
  • For Macro setup dialog, JFrame is now used instead of genericDialog. (not recordable) -- In the dioalog Browsing directory and macro file is now possible.
  • Macro does not close when wrong directory/macro is typed but gives a log message out

1.1.0 (20130215)

Added with Windows Registry reader/writer plugin.


The first version

Something went wrong with that request. Please try again.