Posted by
Cammer, Michael on
Nov 18, 2015; 10:34pm
URL: http://imagej.273.s1.nabble.com/trying-to-open-czi-files-always-opens-entire-set-of-files-in-directory-tp5014974p5014975.html
Actually, I think the problem is solved.
1. Delete or rename the "queue" file
2. Rename the first image file that has no parens and number following it.
Looks like it's working!
=========================================================================
Michael Cammer, Microscopy Core & Skirball Institute, NYU Langone Medical Center
Cell: 914-309-3270 ** Office: Skirball 2nd Floor main office, back right **
http://ocs.med.nyu.edu/microscopy &
http://microscopynotes.com/-----Original Message-----
From: ImageJ Interest Group [mailto:
[hidden email]] On Behalf Of Cammer, Michael
Sent: Wednesday, November 18, 2015 5:35 PM
To:
[hidden email]
Subject: trying to open czi files always opens entire set of files in directory
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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