Run EXE ( IARunEXE )

Runs external program. Input images are exported into a newly created or specified %temp% folder. The program with the given arguments is executed in the %temp% folder. Finally, the images listed in "Result file(s)" are imported. The output of this function is the first result image, and these images are linked to the original images, if x,y,frames dimensions are matching. The channel numbers of the imported result images will start at 101 and be sequentially numbered.

"Use temporary folder": When set to Yes, a unique folder is created for each execution witin the Image Export Folder or in the "Custom (temp) folder", and the %temp% variable will show the full path to this new folder.
This newly created folder is optionally deleted after data has been retrieved. When set to No, the image export and external program runnning is performed in the Image Export Folder, or in the "Custom (temp) folder", if any given, using a full path. The %temp% variable will reflect the Image Export Folder or the Custom temp folder, respectively.

Temporary filenames: Images are exported into the temporary folder before command execution. Two naming schemes are provided - "input#_frame#.ext" and "img_frame#suffix.ext" - where input# is replaced with input image number, and frame# is replaced with frame number. #suffix is replaced with _frame number if no suffixes are given, or with the suffix for each channel that is provided in the "Export input name(es) or suffix(es)" parameter. The ".ext" extension is based on the "Image transfer format" parameter. Each naming scheme can be used with grayscale, RGB or RAW exporting (with constraints of the file type must be considered by the user). Use RGB export for ovrlaid and pseudocolor images.
Filename examples for a single input image export of 3 frames:

1_1.tif; 1_2.tif; 1_3.tif for "input#_frame#.ext"
img_1_1.tif; img_2_1.tif; img_3_1.tif for "img_frame#suffix.ext" when no suffixes are specified.

Arguments: provide a list of arguments to be passed to the executable in the "Arguments" field, separated by spaces. When using multiple CMD window commands in "" and separated by && the arguments will be inserted before the trailing " mark (with a preceding space added).
Argument 1..10: optionally, if these fields are set, these values will follow the corresponding argument from the "Arguments" field. In addition, %arg2%..%arg10% or $arg2$..$arg10$ in these fields will be replaced with the corresponding argument value below, without adding extra spaces. These allow using Argument 1..10 as pipeline parameters. %arg2%..%arg10% cannot have a : separated tag before the clsing % or $.
In looped operation ("Loop for each frame") the external program is executed for each frame, retrieving the result each time. To pass arguments with incrementing frame numbers use %framenumber% is 1 for the first frame. %prevframenumber% is 1 for the first 2 frames, then one less than the %framenumber%. Use %framenumber:3% for 0-padded numbering. During looped operation different arguments may be sent to the external program in each loop. For this provide a list of arguments separated by | . Elements of this list will be used for the corresponding frame. If the list is shorter than the number of frames, the last element of this list is used for any further frames. E.g. Using a list of two arguments allows using one argument for the first frame, and then a different one for any further frames.

Run as Administrator: the external program will be run as Administrator after elevation prompt without image export and import. Use full path in arguments, the program is lauched from the user home folder. Use this option for launching install scripts.
Command windows: hide command windows in the Preferences Misc tab. Override hiding command windows (e.g. for data processing scripts) in the Pipeline Window Options.
Using Run EXE with pipeline parameters: To use user-selectable file or folder names as argument through pipeline parameters select the type of file or folder dialog using the [...] button of the pipeline parameter name.

Example:
Arguments:-first -second -third
Argument 1: 10
Argument 2: 20
Argument 3: 30
will result in: program.exe -first 10 -second 20 -third 30

Example:
Arguments:-first
Argument 1: Function[$arg2$]
Argument 2: 10
will result in: program.exe -first Function[10]

Notes:
Argument 1: \folder\with space\ will result in "\\folder\\with space\\"
Argument 1: =%temp% will result in the path where the images are exported for the external function. Use = mark to trigger expression evaluation.
Inputless operation: this function will run without an input, so a pipeline with inputless Run EXE function does not require an image window present to run.
Note: the %temp% variable cannot be used in the "Path and filename" and in the "Custom temp folder" fields.

Multiple ways of calling python scripts through command line execution:Use the %PythonFolder% variable (start value with = to trigger expression evaluation). Examples using Anaconda:
=""%PythonFolder%Scripts\activate.bat" myenvironment && python -m module" (Suggested way of launching module in myenvironment. Replace myenvironment and module. Note that most pipelines have "-m moudule" as argument parameters.)
=""%PythonFolder%Scripts\activate.bat" myenvironment && "%PythonFolder%\envs\myenvironment\python.exe -m module"" (this allows checking if the module is installed)
=%PythonFolder%envs\myenvironment\python.exe -m module (note: myenvironment is not activated, some features may not work)
=%PythonFolder%envs\myenvironment\scripts\module.exe (note: myenvironment is not activated, some features may not work)
Examples using venv:
=""%PythonFolder%myvenv\Scripts\activate" && python -m module" (Suggested way of launching module in myenv using venv. Replace myvenv and module. Note that most pipelines have "-m moudule" as argument parameters.)
Default Cellpose integration using venv:
=""%ProgramDataFolder%cellpose\scripts\activate" && "python.exe""