Re: Dealing with Nikon .nd2 files

Posted by MORONE Diego RIC on
URL: http://confocal-microscopy-list.275.s1.nabble.com/Limiting-the-z-travel-range-on-Nikon-Ti-tp7582197p7582227.html

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Hi Christian,

the plugin that opens .nd2 files (LOCI Bio-formats importer) is able to read the header information. There's a very active community at imagej listserv

http://list.nih.gov/cgi-bin/wa.exe?LIST=IMAGEJ

In Fiji you could also try Process>Batch>Convert..., with "Read images using Bio-formats" option enabled.

Best,
Diego



................................
Diego Morone
Staff Scientist
Humanitas Clinical and Research Center
Rozzano - Milano, Italy
www.humanitas.it/hur/cms/english/




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-----Original Message-----
From: Confocal Microscopy List [mailto:[hidden email]] On Behalf Of Christian
Sent: giovedì 19 giugno 2014 00:04
To: [hidden email]
Subject: Re: Dealing with Nikon .nd2 files

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Thank you all for the advice.  I will try this macro out, and will admit I have no experience with writing macros.  I have two more questions, is FIJI able to pull the header information off the .nd2 to set scale bars and is there a FIJI discussion group/list serv?

Thanks again, this input will save me many hours of labor.

Christian




________________________________
 From: MORONE Diego RIC <[hidden email]>
To: [hidden email]
Sent: Tuesday, June 17, 2014 4:25 PM
Subject: FW: Dealing with Nikon .nd2 files


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If you have some common tasks like creating a z-projection, you could set up some simple one-click macros and install them on a shared FIJI workstation. Here's a template to convert all files in a directory (untested, adapt to your needs)

--- code ---
path = getDirectory("ND2 Directory"); //load input directory
filelist = getFilelist(path); //load array of all files inside input directory
for (i=0; i< filelist.length; i++) {
    // process nd2 files only
    if (endsWith(filelist[i], ".nd2")) {
        // open file, requires LOCI tools (aka Bio-Formats)
        run("Bio-Formats Importer", "open=" + path + filelist[i] + "autoscale color_mode=Default view=Hyperstack stack_order=XYCZT");
        getDimensions(width,height, channels, slices, frames);
        // create max intensity z-projection
        run("Z Project...", "start=1 stop="+slices+" projection=[Max Intensity]");
        // assign pseudocolors to channels
        for (c=1; c<= channels; c++) {
            Stack.setChannel(c);
            if (c==1) {
                run("Blue");
            } else if (c==2) {
                run("Green");
            } else if (c==3) {
                run("Red");
            }
         }
         // save as multichannel tiff adding a _MAX suffix
         saveAs("TIFF", path+filelist[i]+"_MAX.tif");
    }
}
--- code ---

If you need a primer on macro programming, this could be useful

http://fiji.sc/Introduction_into_Macro_Programming

Best,
Diego

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DAI IL TUO 5x1000 ALLA RICERCA HUMANITAS.

Codice fiscale 10125410158 (Ricerca sanitaria)

http://www.humanitas.it/5x1000
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________________________________________
From: Confocal Microscopy List [[hidden email]] On Behalf Of Christian [[hidden email]]
Sent: Tuesday, June 17, 2014 20:10



To: [hidden email]
Subject: Dealing with Nikon .nd2 files

I am employed in a very diverse multi-user core facility.
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Listers,

I am employed in a very diverse multi-user core facility.  I primarily operate the Nikon A1 between 5 and 7 hours a day for a wide range of users, from undergraduates to PI's.  In any case, the issue I have is that exporting or minor edits to the raw .nd2 files must occur on the A1 system as our users are mostly completely ignorant and we have no imaging software which is not dedicated to a system.  It's amazing how much time I lose trying to export a two channel z-projection from a three channel .nd2.  Do any of you have any suggest software or tutorials I might build upon to provide to my users?  Nearly everything we do is supplementary information (figures), not quantitative, but then I do not believe the users know the difference between an .nd2 and a .jpg.

I have used the FIJI build of ImageJ for some users, but getting folks trained up is also time consuming.  I understand I may be out of luck in this venture.  I do thank you for any help you might provide.

Christian