// Fluorescence Time Trace Extract // This is meant to speed up processing fluorescence imaging data without loading the whole damn file into RAM. That way, you can use it to analyze data on your laptop.... so long as you have a fast internet connection to your data server. // This version frontloads all of the ROI selection so that the slow part of the analysis (opening all the videos and reading out the data) are batched afterwards. This way, the user doesnt need to sit and wait between experiments. // Written by Wilson Adams | Siciliano Lab | Oct 2021 //====================================================== // Step 1: Open File (virtual) [ALREADY OPENED] directory = getDirectory("Choose a directory..."); filelist = getFileList(directory) ; print("Starting Processing: "+directory); Array.show(filelist); processed = 0; //for (i = 0; i < 4; i++) { // FOR TESTING for (i = 0; i < lengthOf(filelist); i++) { if (endsWith(filelist[i], ".tif")) { run("TIFF Virtual Stack...", "open=["+directory + File.separator + filelist[i]+"]"); stk = getTitle(); if (processed == 0) { run("Select All"); roiManager("Add"); // whole image ROI setTool("rectangle"); makeRectangle(437, 272, 490, 457); roiManager("Add"); } runMacro("FluorTime_extract_frontload_dlight.ijm"); print("PROCESSED: "+filelist[i]); processed = processed + 1; } } print("Finished Processing: " + directory);