VSI_to_tiff_macro.ijm

//The following macro code was written by Matthew Jacobs in the Salk Institute's Callaway Neuroscience Lab. 
//It is designed to help convert Olympus Slide Scanner .vsi files into .tif files which can be opened in third party software. 
//This code does not keep 100% of the detail stored in the .vsi, but does give access to the detail scan information in the tif format. 
//There are continuing issues with the autoscaling of the fluorescent chanels, but each channel of the image can be manually scaled after conversion as desired.


//This Creates the dialogue for file extension selection. Really this is only here in case Olympus changes the file extension someday (imagine an updated format called .vsix)
Dialog.create("File type");
Dialog.addString("File suffix: (currently only works with .vsi)", ".vsi", 5);
Dialog.show();
suffix = Dialog.getString();

inDir = getDirectory("Choose Directory Containing " + suffix + " Files ");
outDir = getDirectory("Choose output directory")


//inDir = "F:\\Lab Data\\2024.2.24 OptoITSN Fix Test 1 TIRF\\"
//outDir = "C:\\Users\\Harrison Truscott\\OneDrive - University of North Carolina at Chapel Hill\\Bear Lab\\optotaxis calibration\\data\\tirf calibration local\\2024.2.24 OptoITSN Fix Test 1 TIRF\\"
setBatchMode(true);
processFiles(inDir, outDir, "");
print("Done!");

function processFiles(inBase, outBase, sub) {
  flattenFolders = false; // this flag controls output directory structure
  print("Processing folder: " + inBase + sub);
  list = getFileList(inBase + sub);
  if (!flattenFolders) File.makeDirectory(outBase + sub);
  for (i=0; i<list.length; i++) {
    path = sub + list[i];
    //upath = toUpperCase(path); Leave this line commented out, you only need it if the file extension is case sensitive. Again, this is future proofing against olympus altering the file extension.
    upath = path; //This code was easier to write, and might be replaced by the the previous line (some day) which someone suggested to me.
    if (File.isDirectory(inBase + path)) {
      processFiles(inBase, outBase, path);
      
    }
    else if (endsWith(upath, suffix)) {

    	//print("Importing " + suffix + " = " + list[i] + ", Z-Plane#" + zplane);

		//The top line here does not use the zplane variable to select a focal plane to import. The second line uses the zplane string to selectively import that plane.
		//If you are using a virtual z image, you must select the focal plane you want to import. The top line here will simply use plane #1, which is rarely an in focus image.
		//obsolete command//run("Bio-Formats Importer", "open=["+inBase + path+"] autoscale color_mode=Custom split_channels view=Hyperstack stack_order=XYCZT series_1 series_0_channel_0_red=0 series_0_channel_0_green=0 series_0_channel_0_blue=255 series_0_channel_1_red=0 series_0_channel_1_green=255 series_0_channel_1_blue=0 series_0_channel_2_red=255 series_0_channel_2_green=0 series_0_channel_2_blue=0");
		run("Bio-Formats Importer", "open=["+inBase + path+"] autoscale color_mode=Custom specify_range split_channels view=Hyperstack stack_order=XYCZT series_1 c_begin_1=1 c_end_1=3 c_step_1=1 z_begin_1=zplane z_end_1=zplane z_step_1=0 series_0_channel_0_red=0 series_0_channel_0_green=0 series_0_channel_0_blue=255 series_0_channel_1_red=0 series_0_channel_1_green=255 series_0_channel_1_blue=0 series_0_channel_2_red=255 series_0_channel_2_green=0 series_0_channel_2_blue=0");

		//Saves files in various formats.
		print("Saving .tiff");
		saveAs("Tiff", outBase + path);

		//Prep fiji for the next image by closing open windows and clearing out the cache.
		print("Closing open files...");
		run("Close All");
		
		print("Collecting Garbage...");
		run("Collect Garbage");
    }
  }
}