![]() I'm obviously missing something about how to use imageJ plugins in a programming context. So you need to construct a unique path for the Results for each image. (IJ/runPlugIn imageP "Polar_Transformer" "") 1 In the final line, your script will save a file called Results.csv and then overwrite it when you save the next image. The stupidest way to do what I want is to just close the window that comes up and return the image which it was displaying.ĭoes what I want but is absolutely retarded: (defn x-polar But running this always brings up a window containing the transformed image, when what I want is to simply return the transformed image. Extendable: The functionality of ThunderSTORM can be easily extended to add more features. Support for batch processing: ThunderSTORM takes full advantage of ImageJ's Macro Language which makes batch processing possible (see the example). This is good because it suppresses the dialog which would otherwise pop up for every image. Parallel processing: Processing of the input data is handled in parallel. When to use ImageJ to create a macro When this window is showing, any actions you take in ImageJ will be converted into macro code. For each image in the input folder ImageJ will open the image, apply the commands, save the image to the output folder (if present) and then close the image. There are many analysis routines built in to ImageJ and hundreds more can be freely downloaded from the web. The PROCESSbutton starts the batch processing. The program provides a plugin framework for adding custom functionality. For other kinds of processing, // edit the processFile() function at the end of this macro. This document describes how ImageJ can be used to automate the processing of large numbers of image files in a batch process. In this example, it runs the Subtract // Background command of TIFF files. Use the selectImage (id), isOpen (id) and isActive (id) functions to activate an image or to determine if it is open or active. For the IDs, there's this: getImageID () Returns the unique ID (a negative number) of the active image. (IJ/runPlugIn imageP "Polar_Transformer" ""))) ImageJ is an open source image analysis program. // 'BatchProcessFolders' // // This macro batch processes all the files in a folder and any // subfolders in that folder. ImageJ allows users to reference images using either image titles or image ID numbers. ![]() I find that I can apply a plugin using the following: (defn x-polar Is there a way to take any general imageJ plugin and apply it to hundreds of images automatically?įor example, say I want to take my thousand images and apply a polar transformation to each-Ī polar transformation plugin for ImageJ can be found here: I want to use ImageJ to do some processing of several thousand images.
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