Hello kagebunshin,
I've got some experience with .zvi files and written a simple macro. You
can find some useful info on:
http://wiki.imagej.net/Scripting_toolbox#Opening.2C_processingYou'll need to use Bioformats to open the files.
My little macro will prompt you for a directory containing your files.
With the Zeiss-software you can sometimes change the order for the
channels, so you have to specify that at the beginning (in my case Red,
Green and Blue). In this case I select the 'Blue' channel (ie. the third
channel) to do something with (like analysing particles).
//macro will open all images in same folder, adapted from:
//
http://wiki.imagej.net/Scripting_toolbox#Opening.2C_processing.
//2C_and_saving_a_sequence_of_files_in_a_folder
//print("\\Clear"); //if you want to erase the log window 1st
//Set the channels
Red=1; //Channel 1 is Red, etc.
Green=2;
Blue=3;
//Selecting your files:
imageExtension = ".zvi";
myImagePath = getDirectory("Input directory"); //Dialog asking for folder
imageList = getFileList(myImagePath);
//Processing each file in your directory in turn:
for (i=0; i<imageList.length; i++) {
if (endsWith(imageList[i], imageExtension)) {
fileInfo = myImagePath + imageList[i];
print("Opening \"" + myImagePath + imageList[i] + "\"");
run("Bio-Formats Importer", "open=[" + fileInfo + "]
color_mode=Composite view=Hyperstack stack_order=XYCZT");
//Select channels to work with, corresponding to what was stated at
the beginning of the macro.
Stack.setChannel(Blue);
//Do your things here:
print("Doing nothing yet ...");print("");
//close the image
close();
}
}
print("Finished");
On 07/09/15 14:12, kagebunshin wrote:
> Hello There - I am really not firm with coding and such, so I recorded a
> macro in ImageJ that let's me analyse the area fraction. It looks as
> follows:
>
> open();
> close();
> close();
> setAutoThreshold("Otsu");
> //run("Threshold...");
> setAutoThreshold("Otsu dark");
> run("Analyze Particles...", "size=0-Infinity circularity=0.00-1.00
> show=Nothing display summarize");
> close();
> run("Clear Results");
>
> You're maybe wondering, why there are 2 close-functions - the .ZVI image is
> obtained from a microscope (Zeiss) and has 3 channels. It closes the first 2
> channels ans runs the analysis on the last one, cloeses the image. It's
> fine, opening one image after another but there are hundrets of pictures to
> be analysed. I read through some stuff with GetFileList and such but it
> won't work because it will prompt, that the file-type is not supported or
> anything. Any sugestions or help with that?
> Let's assume the path is "c:\myimagepath" so that even I can follow ;)
> Thanks in advance!!
>
>
>
>
> --
> View this message in context:
http://imagej.1557.x6.nabble.com/Macro-Problem-with-ZVI-Files-tp5014253.html> Sent from the ImageJ mailing list archive at Nabble.com.
>
> --
> ImageJ mailing list:
http://imagej.nih.gov/ij/list.html--
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