Can't open lsm pictures

Hello,

When I try to open .lsm pictures with Cellprofiler on my computer, I get the message: Cellprofiler did not find any image files that matched your matching pattern
If I convert the lsm picture to tiff, it is working.
I am using Windows 7 (32 bit). I tried the pipeline and pictures on other computers with windows 7 (64 bit) and Windows XP (32 bit), in both cases the lsm pictures can be opened without problems. However, on a second computer with Windows 7 (32 bit), I couldn’t open the pictures.

When I start Cellprofiler on my computer, I get the following message:

Traceback (most recent call last):
File “cellprofiler\modules\saveimages.pyc”, line 40, in
File “bioformats_init_.pyc”, line 18, in
File “cellprofiler\utilities\jutil.pyc”, line 155, in
File “cellprofiler\utilities\javabridge.pyc”, line 12, in
File “cellprofiler\utilities\javabridge.pyc”, line 10, in __load
ImportError: DLL load failed: The specified module could not be found.
Failed to load bioformats. SaveImages will not be able to save movies.
could not load these modules (‘cellprofiler.modules.run_imagej’, ImportError(‘D
LL load failed: The specified module could not be found.’,))]
Subversion revision: 10415

Thank you for your help!!

Catherine

Hi Catherine,

It seems like you are dealing with two different problems. Let’s start with the 1st one: being able to open .lsm images. Could you upload the pipeline that is causing problems?

Regards,
-Mark

Hello Mark,

here is my pipeline. It gets stuck in the first step.

Best regards,
Catherine
SBS-modified-lsm4.cp (19.9 KB)

You don’t happen to have a representative .lsm file that you could post also (if it’s not too big)?
-Mark

Hello,

I tried to upload a .lsm file, but it doesn’t work, I get the message “extension lsm is not allowed”

Regards,
Catherine

Can you try renaming the file with an .tif extension and uploading again?
-Mark

Ok, here it is.

Catherine

Thanks! OK, your pipeline/image seems to work on the Windows 7 32-bit installation here, and based on the behavior you’re describing, it seems like you may have a bad CellProfiler installation. Can you try uninstalling CP from your computer and then re-installing?
-Mark

Hello,
thanks for your answer.
I re-installed Cellprofiler, but I still have the same problem.
Catherine

for me it works simply renaming the images from balbla.lsm to blabla.tif

Hi Catherine,

I had a similar error message which was due to a .dll file which was missing on my system. In my case it was msvcr71.dll, which ships with CellProfiler unfortunately, however, it looks for it in the wrong directory :open_mouth:

After copying it from

C:\Program File\CellProfiler\jre\bin\msvcr71.dll
to C:\Program Files\CellProfiler\jre\bin\client\msvcr71.dll

the error message was gone. Maybe you have the same problem?

Btw: I found the missing .dll using Process Monitor technet.microsoft.com/en-en/sysi … s/bb896645 . Just start it, fire up CellProfiler and look for the line where it loads “javabridge.pyc”. The missing .dll should follow shortly after.

Hope that helps.

erik

Hi, sorry to re-hit an old post like this, but I was wondering why I can’t seem to see lsm files using any of my installs of CellProfiler. I don’t see the missing dll file either, or a folder named ‘client’.
Have things changed? Should I be seeing lsm files in bottom left window?

Thanks
Neil

Hi Neil,

No, you won’t see .lsm files in the lower-left panel, since with the current release of CP, it’s not a permissible extension. However, since an LSM file is a special form of TIF, I would suggest following tischer’s suggestion above and renaming them accordingly.

However, the next release of CP (hopefully within the next month) will fully support LSM files, so stay tuned…

Regards,
-Mark