RunImageJ runs an ImageJ command.
ImageJ is an image processing and analysis program (http://rsbweb.nih.gov/ij/). It operates by processing commands that operate on one or more images, possibly modifying the images. ImageJ has a macro language which can be used to program its operation and customize its operation, similar to CellProfiler pipelines. ImageJ maintains a current image and most commands operate on this image, but it's possible to load multiple images into ImageJ and operate on them together.
The RunImageJ module runs one ImageJ command or macro per cycle. It first loads the images you want to process into ImageJ, then runs the command, then retrieves images you want to process further in CellProfiler.
Settings:
Command or macro?
This setting determines whether RunImageJ runs
a command, selected from the list of available commands, or
a macro that you write yourself.
Command:
The command to execute when the module runs.
Macro:
This is the ImageJ macro to be executed. For help on
writing macros, see http://rsb.info.nih.gov/ij/developer/macro/macros.html
Options:
Use this setting to provide options to the command or
macro.
Set the current image?
Check this setting if you want to set the current
ImageJ image using an image from a previous module. Leave it
unchecked to use ImageJ's current image.
Current image:
This is the image that will become ImageJ's current image.
ImageJ commands and macros will perform their operations on this
image. Choose an image produced by a previous module.
Get the current image?
Check this setting if you want to retrieve ImageJ's
current image after running the command or macro. Leave
the setting unchecked if the pipeline does not need to access
the current ImageJ image.
Final image:
This is the name for ImageJ's current image after
processing by the command or macro. The image will be a
snapshot of the current image after the command has run.
Wait for ImageJ?
Some ImageJ commands and macros are interactive; you
may want to adjust the image in ImageJ before continuing. Check
this box to stop CellProfiler while you adjust the image in
ImageJ. Leave the box unchecked to immediately use the image.
This command will not wait if CellProfiler is executed in
batch mode.
Run before each group?
You can run an ImageJ macro or a command before each group of
images. This can be useful in order to set up ImageJ before
processing a stack of images. Choose Nothing if
you do not want to run a command or macro, Command
to choose a command to run or Macro to run a macro.
Command:
The command to execute before processing a group of images.
Macro:
This is the ImageJ macro to be executed before processing
a group of images. For help on writing macros, see
http://rsb.info.nih.gov/ij/developer/macro/macros.html
Run after each group?
You can run an ImageJ macro or a command after each group of
images. This can be used to do some sort of operation on a whole
stack of images that have been accumulated by the group operation.
Choose Nothing if you do not want to run a command or
macro, Command to choose a command to run or
Macro to run a macro.
Command:
The command to execute after processing a group of images.
Macro:
This is the ImageJ macro to be executed after processing
a group of images. For help on writing macros, see
http://rsb.info.nih.gov/ij/developer/macro/macros.html
Save the selected image?
You can save the image that is currently selected in ImageJ
at the end of macro processing and use it later in CellProfiler.
The image will only be available during the last cycle of the
group. Check this setting to use the selected image in CellProfiler
or leave it unchecked if you do not want to use the selected image.
Image name:
This setting names the output image produced by the
ImageJ command or macro that CellProfiler runs after processing
all images in the group. The image is only available at the
last cycle in the group