Re: virtual stack

Posted by Knecht, David on Mar 27, 2010; 5:57pm
URL: http://imagej.273.s1.nabble.com/virtual-stack-tp3688745p3688747.html

Can the time stamper work in hours:min:sec or just hours;min?  It doesn't seem to let me change the time increment to min in order to accomplish this.  Dave

On Mar 22, 2010, at 2:26 AM, Rasband, Wayne (NIH/NIMH) [E] wrote:

> On Mar 21, 2010, at 9:53 AM, David Knecht charter wrote:
>
>> I am trying to add a time stamp to a stack that is too large to open in ImageJ.  I added the Time Stamper plugin to a virtual stack macro to try to get it to do the job, but I get back an error message that the file is not a stack.  How do you get around this?  Dave
>
> You can time stamp a virtual stack by using the Process>Batch>Macro command and entering macro code something like this:
>
>   setFont("SansSerif", 18, "antialiased");
>   setColor("white");
>   n=toString(i);
>   while (lengthOf(n)<4) n="0"+n;
>   drawString(n, 20, 30);
>
> The Process>Batch>Macro command was added in ImageJ 1.43.
>
> -wayne
>
>
>> // Process Virtual Stack
>> //
>> // This macro demonstrates how to process the images in a
>> // virtual stack, save the processed images in a folder, and
>> // then open those images in another virtual stack. The virtual
>> // stack can be opened using File>Import>Image Sequence,
>> // File>Import>TIFF Virtual Stack or File>Import>Raw.
>>
>> if (nSlices==1) exit("Stack required");
>> dir = getDirectory("Choose Destination Directory ");
>> setBatchMode(true);
>> id = getImageID;
>> for (i=1; i<= nSlices; i++) {
>>     showProgress(i, nSlices);
>>     selectImage(id);
>>     setSlice(i);
>>     name = getMetadata;
>>     run("Duplicate...", "title=temp");
>>     run("Time Stamper");
>>     saveAs("tif", dir+pad(i-1));
>>     close();
>> }
>> setBatchMode(false);
>> run("Image Sequence...", "open=["+dir+"00000.tif] use");
>>
>> function pad(n) {
>>     str = toString(n);
>>     while (lengthOf(str)<5)
>>         str = "0" + str;
>>     return str;
>> }
>>
>> Dr. David Knecht    
>> Department of Molecular and Cell Biology
>> Co-head Flow Cytometry and Confocal Microscopy Facility
>> U-3125
>> 91 N. Eagleville Rd.
>> University of Connecticut
>> Storrs, CT 06269
>> 860-486-2200
>> 860-486-4331 (fax)

Dr. David Knecht    
Department of Molecular and Cell Biology
Co-head Flow Cytometry and Confocal Microscopy Facility
U-3125
91 N. Eagleville Rd.
University of Connecticut
Storrs, CT 06269
860-486-2200
860-486-4331 (fax)