http://imagej.273.s1.nabble.com/trying-to-open-czi-files-always-opens-entire-set-of-files-in-directory-tp5014974p5014976.html
stacks. It will create a folder in your indicated output directory for
channels.
> We are having a problem with LOCI tools opening .czi files from Zeiss
> Lightsheet.Z1. The problem is that when we select any single file, LOCI
> attempts to open all the files into one big dataset.
>
>
>
> The directory is full of multichannel Z series each recorded at a
> sequential timepoint.
>
>
>
> We want to open each one individually, process it, and then save a new tif
> file with the processed data.
>
>
>
> The problem is that LOCI always tries to open the entire sequence at once.
>
>
>
> We have tried different options such as
>
> openPath = getDirectory("Choose a Directory");
> fileList = getFileList(openPath);
> for (i=0; i<fileList.length; i++) {
> if ( (endsWith(fileList[i], ".czi")) || (endsWith(fileList[i], ".nd2"
> )) ) {
> run("Bio-Formats Importer", "open='" + openPath + fileList[i] + "'
> color_mode=Default view=[Standard ImageJ] stack_order=Default ");
>
>
>
> where we expected "Standard ImageJ" to be the least likely to open
> multiple files at once.
>
>
>
> We've found that renaming files works so that they don't make a sequence,
> but with a lot of files, changing the root name is not practical.
> Actually, renaming the first file on one of our computers works for the
> entire sequence but not on another one! We have tried old versions and
> today's daily build of LOCI plugins.
>
>
>
> Is there a way to turn off opening multiple files?
>
>
>
> Any help appreciated. Including if there is a way from Zen to do this,
> but it only appears to have options to write out individual tifs or the
> entire volume, not the individual Z stacks.
>
>
>
> What the directory looks like:
>
>
>
> Directory of E:\SWAP\20151109\overnight_20151109to10\view2
>
> 11/09/2015 06:24 PM 3,023,376,608 Covernight_G2(1).czi
> 11/09/2015 06:52 PM 3,023,330,432 Covernight_G2(10).czi
> 11/10/2015 12:52 AM 3,023,240,544 Covernight_G2(100).czi
> ...
> 11/10/2015 12:44 AM 3,023,205,920 Covernight_G2(98).czi
> 11/10/2015 12:48 AM 3,023,393,600 Covernight_G2(99).czi
> 11/10/2015 07:24 AM 3,023,266,784 Covernight_G2.czi
> 11/10/2015 07:24 AM 4,687 Covernight_G2.queue
> 201 File(s) 604,661,886,415 bytes
> 2 Dir(s) 4,414,754,717,696 bytes free
>
> Thank you!!
>
>
>
>
> _________________________________________
> Michael Cammer, Optical Microscopy Specialist
>
http://ocs.med.nyu.edu/microscopy>
http://microscopynotes.com/> Cell: (914) 309-3270
>
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