Can't open lsm pictures


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!!


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?


Hello Mark,

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

Best regards,
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)?


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


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

Ok, here it is.


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?

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

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 … 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.


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?


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…