trying to open czi files always opens entire set of files in directory

[Cammer, Michael]

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: [phone]

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[Cammer, Michael]

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: [phone]

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[Douglas Richardson]

Hi Michael,

Here is a macro we wrote that breaks the .czi file into multiple .tif
stacks.  It will create a folder in your indicated output directory for
each channel and will place a file for each timepoint and view/angle in
those folders:

http://hcbi.fas.harvard.edu/lightsheet-czi-tif-converter-timelapsemultiview

If you don't want to process the entire file, the following macro command
lets you open specific timepoints/views:

//Angle = a variable representing the view/angle you want to open
//Time = a variable representing the timepoint you want to open
//This defaults to open all channels, but you could also specify individual
channels.

run("Bio-Formats Importer", "open=" + filePath + " color_mode=Grayscale
specify_range view=Hyperstack stack_order=XYCZT series_" + Angle + "
t_begin_" + Angle + "=" + Time + " t_end_" + Angle + "=" + Time + "
t_step_" + Angle + "=1");



Hope this helps,

-Doug

On Wed, Nov 18, 2015 at 5:34 PM, Cammer, Michael <[hidden email]
> wrote:

> 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: [phone]
>
> ------------------------------------------------------------
> This email message, including any attachments, is for the sole use of the
> intended recipient(s) and may contain information that is proprietary,
> confidential, and exempt from disclosure under applicable law. Any
> unauthorized review, use, disclosure, or distribution is prohibited. If you
> have received this email in error please notify the sender by return email
> and delete the original message. Please note, the recipient should check
> this email and any attachments for the presence of viruses. The
> organization accepts no liability for any damage caused by any virus
> transmitted by this email.
> =================================
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

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[Sebastian Rhode-5]

Hi Guys,

maybe I observed a similar or at least related issue a non-lightsheet CZI file. The file ends with _pt68.czi.

When I try to open this one via BioFormats 5.1.6, BF first complains that the file is too large (65MB ???).  And if you than select the option Virtual stack the result has 68 Channels (but the CZI has only one channel). Also the OME_XML looks strange.

Now delete the _pt68 from the filename and try the same - and it works fine. The file has 1 channel and the size is 65MB. And the OME-XML looks OK.

Has anyone a clue if the is related to some issues in BioFormats 5.1.6 or anything else?

Cheers,  Sebi

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[ctrueden]

Please report these issues to the OME Bio-Formats team.

Thanks,
Curtis
On Nov 19, 2015 1:24 AM, "Sebastian Rhode" <
[hidden email]> wrote:

> Hi Guys,
>
> maybe I observed a similar or at least related issue a non-lightsheet CZI
> file. The file ends with _pt68.czi.
>
> When I try to open this one via BioFormats 5.1.6, BF first complains that
> the file is too large (65MB ???).  And if you than select the option
> Virtual stack the result has 68 Channels (but the CZI has only one
> channel). Also the OME_XML looks strange.
>
> Now delete the _pt68 from the filename and try the same - and it works
> fine. The file has 1 channel and the size is 65MB. And the OME-XML looks OK.
>
> Has anyone a clue if the is related to some issues in BioFormats 5.1.6 or
> anything else?
>
> Cheers,  Sebi
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

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