As @Kristian pointed out, @
can help here. It also appears that there may be some extra or misplaced \"
in the code above. This seems to give the desired output string:
string fijiExeFile = @"D:\fiji-win64\Fiji.app\ImageJ-win64.exe";
string fileName = @"D:\\Output\\Untitiled032\\ChanA_0001_0001_0001_0001.tif";
string bioformats = "Bio-Formats";
string options = string.Format("open={0} display_ome-xml", fileName);
string runCommand = string.Format("run('{0}','{1}')", bioformats, options);
string fijiCmdText = string.Format("\"{0}\" -eval \"{1}\"", fijiExeFile, runCommand);