// Batch neurite length measurement - skeletonization method setBatchMode(true); dir = getDirectory("Choose source directory"); output = getDirectory("Choose output directory"); list = getFileList(dir); for (i=0; i<list.length; i++) if(endsWith(list[i], ".tif")) open(dir + list[i]); // Preprocessing run("8-bit"); run("Subtract Background", "rolling=50"); run("Enhance Contrast", "saturated=0.35"); setAutoThreshold("Default"); run("Convert to Mask"); run("Skeletonize"); // Measure skeleton run("Analyze Skeleton (2D/3D)"); saveAs("Results", output + list[i] + "_skeleton.csv"); close();
If you provide your (e.g., phase contrast, DIV7 cortical neurons, 40x) and whether you need total neurite length per cell or average neurite length , I can tailor the macro or tracing settings further. neurite length measurement imagej
: Open your image and navigate to Analyze > Set Scale . // Batch neurite length measurement - skeletonization method
Neurite length measurement can be done in three ways with ImageJ: dir = getDirectory("Choose source directory")
| Task | Shortcut / Menu | |------|----------------| | Set scale | Analyze > Set Scale | | Manual trace | Segmented Line tool → M | | NeuronJ trace | Plugins > NeuronJ → New → click along neurite | | Batch macro | Plugins > New > Macro → paste code → Run | | Save results | Results window → File > Save As | | Calibrate from image | Known distance (µm) / pixels |