How to load tiff movies?

hello,
I am greenhand.
I want to load tiff file which contains a series of images as individual frames.And I came across a question.I can’t load it.
error information:
Traceback (most recent call last):
File “cellprofiler\pipeline.pyc”, line 1238, in prepare_run
File “cellprofiler\modules\loadimages.pyc”, line 1397, in prepare_run
File “cellprofiler\modules\loadimages.pyc”, line 1822, in prepare_run_of_flex
File “cellprofiler\utilities\jutil.pyc”, line 439, in method
File “cellprofiler\utilities\jutil.pyc”, line 377, in call
JavaException: Index: 0, Size: 0

my final goal is identify cells from 3D image data and I regard the tiff file as a 3D image file. it’s difficult to me so I need help.
Thanks.

Hi,

If I’m not mistaken, this thread might answer your question (in particular, this part). Let us know if this doens’t solve your problem.

Cheers,
-Mark

Hi,
I have installed latest trunk build.It is CellProfiler_2.0.0_win64_r20120829204836.exe. It shows : error prepare while preparing for run :failed to get image set.
I installed CellProfiler_2.0_win64_r11710.exe yesterday. I think I input wrong regular expression.So now I decide to load a series of tif pictures.they are named as test00***.tif. *** are three numbers. There are 200 pictures at least. And many manipulations need to be repeated many times.For example, how do I filter 200 pictures in 20 times?
And I wonder it whether cellprofiler could identify 3D cells from a series of tif pictures(these tif pictures are from a 3D image).

[quote=“lpsl1882”]Hi,
I have installed latest trunk build.It is CellProfiler_2.0.0_win64_r20120829204836.exe. It shows : error prepare while preparing for run :failed to get image set.
I installed CellProfiler_2.0_win64_r11710.exe yesterday. I think I input wrong regular expression.So now I decide to load a series of tif pictures.they are named as test00***.tif. *** are three numbers. There are 200 pictures at least. And many manipulations need to be repeated many times.For example, how do I filter 200 pictures in 20 times?[/quote]

You can load the images in LoadImages and group them according to stack if you organize the each stack into a separate sub-folder, point the default image folder to the root folder and specify “All” for “Analyze all sub-folders…” in LoadImages. Then you can extract metadata specifying the sub-folder name from the Path, check the “Group images by metadata” and select the metadata that corresponds to the sub-folder.

You can see an example of this approach in our Examples page; search for “Object Tracking and Metadata Management” on that page.

By any chance, can you upload the original TIF stack of images to this forum thread?

Unfortunately, 3-D segmentation is not one of CellProfiler’s capabilities. You could use CellProfiler to create a 2_D projection from a 3-D stack and detect cells from that 2-D image, but that would require that the cells be stationary in (x,y) and not overlap in the z-dimension.

Regards,
-Mark

oh, I see