//Macro_Opera_Channel_Splitter_MaxProjection macroName = "Opera_Channel_Splitter_MaxProjection"; macroShortDescription = "This macro splits channels from Opera microscope .flex images and does a maximum projection per channel."; macroDescription = "This macro splits up to 5 channels per field acquired with Opera automated microscope and saves individual .tif." + "\nIf channels have multiple planes, a maximum Z-projection per channel is performed. Define channel tags for .tif." + "\nImage order: e.g. Ch1-z1, Ch1-z2, Ch1-z3, Ch2-z1, Ch2-z2, Ch2-z3, Ch3-z1, ..."; macroRelease = "first release 29-08-2014 by Marc Bickle and Martin Stöter (stoeter(at)mpi-cbg.de)"; macroHelpURL = "http://idisk-srv1.mpi-cbg.de/knime/FijiUpdate/TDS%20macros/" + macroName + ".htm"; macroHtml = "" +"" + macroName + "/n" + macroRelease + "
" +"Check for help on this web page:
" +"" + macroHelpURL + "
" +"...get this URL from Log window!
" +""; //print macro name and current time to Log window getDateAndTime(year, month, dayOfWeek, dayOfMonth, hour, minute, second, msec); month++; print("\\Clear"); print(macroName,"\nStart:",year+"-"+month+"-"+dayOfMonth+", h"+hour+"-m"+minute+"-s"+second); print(macroHelpURL); //start macro Dialog.create("Fiji macro: " + macroName); Dialog.addMessage("Fiji macro: " + macroName + " (Fiji-Tools-for-HCS by TDS@MPI-CBG)\n \n" + macroShortDescription + "\nClick 'OK' to go on, 'Cancel' to quit or 'Help' for online description."); Dialog.addHelp(macroHtml); Dialog.show; //choose folders inputPath = getDirectory("Choose image folder... "); outputPath = getDirectory("Choose result image folder... or create a folder"); printPaths = "inputPath = \"" + inputPath + "\";\noutputPath = \"" + outputPath + "\";"; print(printPaths); //set log file number tempLogFileNumber = 1; while (File.exists(outputPath + "Log_temp_" + tempLogFileNumber +".txt")) tempLogFileNumber ++; //find last tempLog file to prevent overwriting of log //initialize => default settings run("Set Measurements...", "area mean standard min centroid center shape integrated median display redirect=None decimal=3"); run("Input/Output...", "jpeg=95 gif=-1 file=.txt copy_column copy_row save_column save_row"); run("Close All"); run("Color Balance..."); //////////////////////////////// M A C R O C O D E /////////////////////////////// //set array variables imageSuffix = newArray("Ch1", "Ch2", "Ch3", "Ch4", "Ch5"); //array of default channel names imageSuffix = newArray("ZO1", "CD13", "DAPI", "Ch4", "Ch5"); planesPerChannelArray = newArray(3, 3, 1, 1, 1); //array of planes per channel manualMode = true; batchMode = false; imageNumberPerField = 0; numberOfChannels = 0; //get file list and well list fileList = getFileList(inputPath); Array.sort(fileList); while (!(numberOfChannels > 0 && numberOfChannels <= 5)) { //must be 1-5 channels Dialog.create("How many channels!"); //enable use inveractivity Dialog.addNumber("Number of channels in .flex?", 3); //if checked macro will run automatically Dialog.show(); numberOfChannels = Dialog.getNumber(); } Dialog.create("How many planes per channel"); //enable use inveractivity for (currentChannel = 1; currentChannel <= numberOfChannels; currentChannel++) { Dialog.addNumber("Number of planes in channel " + currentChannel + ":", planesPerChannelArray[currentChannel-1]); } for (currentChannel = 1; currentChannel <= numberOfChannels; currentChannel++) { Dialog.addString("Channel " + currentChannel + ", tag: ", imageSuffix[currentChannel-1]); } Dialog.addCheckbox("Set batch mode (hide images)?", batchMode); //if checke no images will be displayed Dialog.show(); for (currentChannel = 1; currentChannel <= numberOfChannels; currentChannel++) { planesPerChannelArray[currentChannel-1] = Dialog.getNumber(); imageNumberPerField = imageNumberPerField + planesPerChannelArray[currentChannel-1]; } for (currentChannel = 1; currentChannel <= numberOfChannels; currentChannel++) imageSuffix[currentChannel-1] = Dialog.getString(); batchMode = Dialog.getCheckbox(); //go through all file for (currentFile = 0; currentFile < fileList.length; currentFile++) { if (endsWith(fileList[currentFile],".flex")) { //check if it is right file and handle error on open() showProgress(currentFile/fileList.length); showStatus("processing " + fileList[currentFile]); setBatchMode(!manualMode & batchMode); IJ.redirectErrorMessages(); run("TIFF Virtual Stack...", "open=" + inputPath + fileList[currentFile]); showProgress(currentFile / fileList.length); showStatus("processing" + fileList[currentFile]); if (nImages > 0) { //if image is open getDimensions(width, height, channels, slices, frames); //print(width, height, channels, slices, frames); print("opened (" + (currentFile + 1) + "/" + fileList.length + "):", fileList[currentFile], ", channels =", channels); //to log window for (currentField = 1; currentField <= slices/imageNumberPerField; currentField++) { //now iterate through all channel and save as .tif using selected tags firstImageInChannel = 1; lastImageInChannel = 0; for (currentChannel = 1; currentChannel <= numberOfChannels; currentChannel++) { selectWindow(fileList[currentFile]); lastImageInChannel = lastImageInChannel + planesPerChannelArray[currentChannel-1]; //print(currentField,currentChannel,planesPerChannelArray[currentChannel-1],firstImageInChannel,lastImageInChannel); run("Make Substack...", "slices=" + ((currentField-1) * imageNumberPerField + firstImageInChannel) + "-" + ((currentField-1) * imageNumberPerField + lastImageInChannel)); subStackID = getTitle(); if (planesPerChannelArray[currentChannel-1] > 1) run("Z Project...", "start=1 stop=" + planesPerChannelArray[currentChannel-1] + " projection=[Max Intensity]"); saveAs("Tiff", outputPath + substring(fileList[currentFile],0,9) + "_f" + currentField + "_" + imageSuffix[currentChannel-1] + ".tif"); print("saved substack (" + ((currentField-1) * imageNumberPerField + firstImageInChannel) + "-" + ((currentField-1) * imageNumberPerField + lastImageInChannel) + "):", substring(fileList[currentFile],0,9) + "_f" + currentField + "_" + imageSuffix[currentChannel-1] + ".tif"); close(); //Z-projection close(subStackID); //substack firstImageInChannel = firstImageInChannel + planesPerChannelArray[currentChannel-1]; } } close(fileList[currentFile]); //.flex } else { //if no images open print("file (" + (currentFile + 1) + "/" + fileList.length + "): ", fileList[currentFile], " could not be opened."); //if open() error } } else { //if file has different extensionn print("file (" + (currentFile + 1) + "/" + fileList.length + "): ", fileList[currentFile], " was skipped."); //if not .lsm } } //print current time to Log window and save log getDateAndTime(year, month, dayOfWeek, dayOfMonth, hour, minute, second, msec); month++; print("Macro executed successfully.\nEnd:",year+"-"+month+"-"+dayOfMonth+", h"+hour+"-m"+minute+"-s"+second); selectWindow("Log"); saveAs("Text", outputPath + "Log_"+year+"-"+month+"-"+dayOfMonth+", h"+hour+"-m"+minute+"-s"+second+".txt"); if (File.exists(outputPath + "Log_temp_" + tempLogFileNumber +".txt")) File.delete(outputPath + "Log_temp_" + tempLogFileNumber + ".txt"); //delete current tempLog file //////////////////////////////////////// E N D O F M A C R O ////////////////////////////