Loading .zvi files

I am new and see reference in the manual to being able to load .zvi files, but I have yet to figure out how to do this. According to the manual this is possible, but I can’t be certain this statement belongs to CellProfiler 2.0. I tried changing my extension from .zvi to .ZVI because of comments on case sensitivity, but it is apparently not that simple.

I found reference to an ImageJRun module or some such and thought maybe there would be a way to use Loci Biorformats to help. I can’t find such a module. My images are simple 1 panel grayscale images for now.

Ultimately, I’d also like to work with Leica .lif confocal images so being able to call upon and use Bioformats would be really useful. Are there any modules to help or am I stuck doing batch conversions in some other program?

Thanks.

By the way,here is pyton output, when trying to run ExampleWouldnHealing.cp pipline on my series of images. Does this help clarify something I might be doing wrong?

Load ilastik Core
Traceback (most recent call last):
File “cellprofiler\modules\loadimages.pyc”, line 60, in
File “bioformats_init_.pyc”, line 19, in
File “cellprofiler\utilities\jutil.pyc”, line 159, in
File “cellprofiler\utilities\javabridge.pyc”, line 12, in
File “cellprofiler\utilities\javabridge.pyc”, line 10, in load
ImportError: DLL load failed: %1 is not a valid Win32 application.
Traceback (most recent call last):
File "cellprofiler\modules_init
.pyc", line 298, in add_module
File “cellprofiler\modules\run_imagej.pyc”, line 21, in
File "bioformats_init
.pyc", line 19, in
File “cellprofiler\utilities\jutil.pyc”, line 159, in
File “cellprofiler\utilities\javabridge.pyc”, line 12, in
File “cellprofiler\utilities\javabridge.pyc”, line 10, in _load
ImportError: DLL load failed: %1 is not a valid Win32 application.
None
Traceback (most recent call last):
File “cellprofiler\modules\saveimages.pyc”, line 40, in
File "bioformats_init
.pyc", line 19, in
File “cellprofiler\utilities\jutil.pyc”, line 159, in
File “cellprofiler\utilities\javabridge.pyc”, line 12, in
File “cellprofiler\utilities\javabridge.pyc”, line 10, in __load
ImportError: DLL load failed: %1 is not a valid Win32 application.
Failed to load bioformats. SaveImages will not be able to save movies.

Adding Hessian matrix of Gaussian to Group Orientation
Adding Eigenvalues of Hessian matrix of Gaussian to Group Texture
Adding Eigenvalues of structure tensor to Group Texture
Adding Gradient Magnitude of Gaussian to Group Edge
Adding Gaussian Smoothing to Group Color
Adding Structure Tensor to Group Orientation
Adding Laplacian of Gaussian to Group Edge
Adding Difference of Gaussians to Group Edge
Loaded classifier: Random forest classifier
Loaded classifier: Random forest classifier (stable)
Loaded classifier: Random forest classifier with variable importance
could not load these modules (‘cellprofiler.modules.run_imagej’, ImportError(‘D
LL load failed: %1 is not a valid Win32 application.’,))]
Subversion revision: 11710
Pipeline saved with CellProfiler SVN revision 11710
Traceback (most recent call last):
File “cellprofiler\pipeline.pyc”, line 309, in run
File “cellprofiler\modules\loadimages.pyc”, line 2075, in run
File “cellprofiler\modules\loadimages.pyc”, line 2770, in provide_image
File “cellprofiler\modules\loadimages.pyc”, line 2808, in load_using_PIL
File “Image.pyc”, line 1982, in open
IOError: cannot identify image file
Thu Jul 11 15:01:37 2013: Image # 1, module LoadImages # 1: 0.02 sec (bg)
Traceback (most recent call last):
File “cellprofiler\pipeline.pyc”, line 309, in run
File “cellprofiler\modules\colortogray.pyc”, line 265, in run
File “cellprofiler\cpimage.pyc”, line 524, in get_image
File “cellprofiler\modules\loadimages.pyc”, line 2770, in provide_image
File “cellprofiler\modules\loadimages.pyc”, line 2808, in load_using_PIL
File “Image.pyc”, line 1982, in open
IOError: cannot identify image file
Thu Jul 11 15:01:49 2013: Image # 1, module ColorToGray # 2: 0.00 sec (bg)

Hi,

In LoadImages, you should change the first setting to choose “tif, tiff, flex, zvi movies”. Did you? You will then get different settings to parse out the channels in the zvi file. If you post your pipeline file, it helps us to clear up any confusion.

Also, using Bioformats is a good idea, and CP uses it automatically! You don’t have to do anything, and can even see that in your error output.

“RunImageJ” is the name of the CP ImageJ module. Do you need ImageJ?

I am concerned about the “ImportError: DLL load failed: %1 is not a valid Win32 application” error. It might be solved by the ZVI setting mentioned above, but it could also indicate something wrong with your installation, or a missing DLL file on your Windows machine.
If you still have troubles, please post (1) an example zvi file, possibly with Dropbox if the forum does not allow that file type and (2) your current .cp pipeline file

Thanks,
David

Sorry for the sloppy way I documented things so far, chalk it up to “newness confusion”…

A couple of background context piece:
OS Windows 7 - Enterprise - 64 bit
Python 2.7 and Python 3.3 installed natively along with some other python libraries
(although I thought Cell Profiler used its own python engine?)
As of Previous post: Fiji - Win 64 version of ImageJ installed
Now I have added (if it matters) and unzipped version of native ImageJ.
I have Java 7 update 21 and Java 7 update 21 (64-bit)

I will attach the ExampleWoundHealing.cp Pipeline I was playing with. The main modifications are the input and output directories and trying to make the file type .zvi. I will also attach a .zvi which is among those that are giving me problems.

I wrote a macro to batch convert the images to .tif using FIJI, and the images at least load and are pseudoprocessed (meaning I haven’t played with the pipeline per se, just tested that processing begins). In the FIJI context Loci bioformats loads the images fine. They are single grayscale images.
ExampleWoundHealing.cp (6.2 KB)

Hi,

Is all going well with CP for you now? I wasn’t sure if you had particular questions in this last post.

Comments:

  • Do you need to use the Developer’s version of CP? You reference python, but can you not just use the compiled version and not run into potential python pitfalls?
  • You do not need ImageJ or FIJI for CP to work. RunImageJ will launch its own copy of ImageJ.
  • Your Java should be fine. Are you still having ZVI issues?
  • You did not attach the example ZVI. If the Forum restricts that file type, try zipping it or upload via Dropbox, etc.
  • Is there something that you want us to look at in the attached pipeline?

Thanks,
David