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CU-MacroLibrary\n## ImageJ2 macro library with variables and functions\n[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.4885048.svg)](https://doi.org/10.5281/zenodo.4885048)\n\n### Software requirements\nCU-MacroLibrary requires a recent version of the [Fiji](https://fiji.sc/) image processing package:\n* ImageJ2 executable (\u003e= 1.53e)\n* Bio-Formats plugin (\u003e= 6.4.0)\n\n### Software installation\nTo install the CU-MacroLibrary with your copy of Fiji, simply copy the `Library.txt`\nto `Fiji.app\\macros\\` and its content will be available to any executed or installed macro.\nIn addition, ImageJ2's macro editor will autocomplete function names from the library.\n\n### Available macro functions (selection)\n* [**`endsWithEither`**](https://github.com/christianrickert/CU-MacroLibrary/blob/main/Library.txt#L91): simple test if a string ends with suffixes from a list.\n* [**`getFilesInFolder`**](https://github.com/christianrickert/CU-MacroLibrary/blob/main/Library.txt#L150): returns a list of files matching a suffix patterns.\n* [**`getMedian`**](https://github.com/christianrickert/CU-MacroLibrary/blob/main/Library.txt#L176): calculates the median value within given threshold values.\n* [**`getMedianValue`**](https://github.com/christianrickert/CU-MacroLibrary/blob/main/Library.txt#L197): calculates the median value for a given array.\n* [**`getRegionOverlap`**](https://github.com/christianrickert/CU-MacroLibrary/blob/main/Library.txt#L253): calculates the relative overlap between two ROI Manager regions.\n* [**`getRoisFromMasks`**](https://github.com/christianrickert/CU-MacroLibrary/blob/main/Library.txt#L284): populates the ROI Manager with regions identified from a segmentation mask.\n* [**`normalizePixelValues`**](https://github.com/christianrickert/CU-MacroLibrary/blob/main/Library.txt#L575): normalizes the pixel intensities of an image by its median value.\n* [**`readImage`**](https://github.com/christianrickert/CU-MacroLibrary/blob/main/Library.txt#L605): reads image files with Bio-Format and labels the slices with the channel names.\n* [**`rescalePixelValues`**](https://github.com/christianrickert/CU-MacroLibrary/blob/main/Library.txt#L684): rescales pixel intensities to a custom range, including `NaN` values.\n* [**`setMasksFromRois`**](https://github.com/christianrickert/CU-MacroLibrary/blob/main/Library.txt#L753): creates a segmentation mask from available ROI Manager regions.\n* [**`substractRegions`**](https://github.com/christianrickert/CU-MacroLibrary/blob/main/Library.txt#L829): implements the missing `Substract` function for the ROI Manager.\n* [**`toggleBatchMode`**](https://github.com/christianrickert/CU-MacroLibrary/blob/main/Library.txt#L854): improves performance for image processing, selections, and ROI Manager updates.\n* [**`waitForWindow`**](https://github.com/christianrickert/CU-MacroLibrary/blob/main/Library.txt#L962): halts the macro progression until a window with a specific title is available.\n\n### Copyright notices\nThe [ImageJ2 image](https://github.com/imagej/imagej.github.io/blob/main/media/icons/imagej-shadow.png) is part of the [GitHub Pages for ImageJ](https://github.com/imagej/imagej.github.io).\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fhimsr-lab%2Fcu-macrolibrary","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fhimsr-lab%2Fcu-macrolibrary","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fhimsr-lab%2Fcu-macrolibrary/lists"}