Cannot open image files in cellprofiler

First of all, thank you for your work on this amazing image analysis software – I am a hematopathologist working with 3 color fluorescence-stained bone marrow biopsies in tissue microarray format, and from my perspective the combination of CP and CPA can potentially function like flow cytometry on a tissue microarray slide and then some. I’ve just installed the most recent profiler and profiler analyst and sqlite on my home computer, worked through some of the examples, downloaded a few of my images (3 color fluorescence) from the stanford tissue microarray database (tif format), built a pipeline, and hit go and… nothing. so then i tried to just open one of the downloaded tif files with cell profiler and again nothing. also nothing with the jpeg file, or the separated out grayscale blue channel image, or a png version. these files open just fine in photoshop and other viewers, and the example tif files from the cellprofiler website open fine in profiler. what the heck am i doing wrong?

I get memory error messages when I try to open my files within cell profiler, although according to task manager I have close to a gigabyte of memory available throughout the process. However cell profiler uses about 0.4GB of RAM just sitting there looking pretty, which seems ominous. I’ve been trying this on my home computer: Windows XP Professional version 2002, Pentium 3.00GHz, 2.00 GB of RAM

I’ve pasted an example of the error message I get just from trying to open an image file within cell profiler below.

Is my computer not up to the task? Is the installation off somehow?

I appreciate your input, Dita

MemoryError
Traceback (most recent call last):
File “cellprofiler\gui\cpfigure.pyc”, line 269, in on_paint
File “matplotlib\backends\backend_wxagg.pyc”, line 59, in draw
File “matplotlib\backends\backend_agg.pyc”, line 314, in draw
File “matplotlib\artist.pyc”, line 46, in draw_wrapper
File “matplotlib\figure.pyc”, line 773, in draw
File “matplotlib\artist.pyc”, line 46, in draw_wrapper
File “matplotlib\axes.pyc”, line 1701, in draw
File “matplotlib\artist.pyc”, line 46, in draw_wrapper
File “matplotlib\image.pyc”, line 237, in draw
File “matplotlib\image.pyc”, line 182, in make_image
File “matplotlib\cm.pyc”, line 167, in to_rgba
File “matplotlib\colors.pyc”, line 527, in call
MemoryError
Traceback (most recent call last):
File “cellprofiler\gui\cpfigure.pyc”, line 269, in on_paint
File “matplotlib\backends\backend_wxagg.pyc”, line 59, in draw
File “matplotlib\backends\backend_agg.pyc”, line 314, in draw
File “matplotlib\artist.pyc”, line 46, in draw_wrapper
File “matplotlib\figure.pyc”, line 773, in draw
File “matplotlib\artist.pyc”, line 46, in draw_wrapper
File “matplotlib\axes.pyc”, line 1701, in draw
File “matplotlib\artist.pyc”, line 46, in draw_wrapper
File “matplotlib\image.pyc”, line 237, in draw
File “matplotlib\image.pyc”, line 182, in make_image
File “matplotlib\cm.pyc”, line 167, in to_rgba
File “matplotlib\colors.pyc”, line 527, in call
MemoryError
Traceback (most recent call last):
File “cellprofiler\gui\cpfigure.pyc”, line 269, in on_paint
File “matplotlib\backends\backend_wxagg.pyc”, line 59, in draw
File “matplotlib\backends\backend_agg.pyc”, line 314, in draw
File “matplotlib\artist.pyc”, line 46, in draw_wrapper
File “matplotlib\figure.pyc”, line 773, in draw
File “matplotlib\artist.pyc”, line 46, in draw_wrapper
File “matplotlib\axes.pyc”, line 1701, in draw
File “matplotlib\artist.pyc”, line 46, in draw_wrapper
File “matplotlib\image.pyc”, line 237, in draw
File “matplotlib\image.pyc”, line 182, in make_image
File “matplotlib\cm.pyc”, line 167, in to_rgba
File “matplotlib\colors.pyc”, line 527, in call
MemoryError
Traceback (most recent call last):
File “cellprofiler\gui\cpfigure.pyc”, line 269, in on_paint
File “matplotlib\backends\backend_wxagg.pyc”, line 59, in draw
File “matplotlib\backends\backend_agg.pyc”, line 314, in draw
File “matplotlib\artist.pyc”, line 46, in draw_wrapper
File “matplotlib\figure.pyc”, line 773, in draw
File “matplotlib\artist.pyc”, line 46, in draw_wrapper
File “matplotlib\axes.pyc”, line 1701, in draw
File “matplotlib\artist.pyc”, line 46, in draw_wrapper
File “matplotlib\image.pyc”, line 237, in draw
File “matplotlib\image.pyc”, line 182, in make_image
File “matplotlib\cm.pyc”, line 167, in to_rgba
File “matplotlib\colors.pyc”, line 527, in call
MemoryError
Traceback (most recent call last):
File “cellprofiler\gui\cpfigure.pyc”, line 269, in on_paint
File “matplotlib\backends\backend_wxagg.pyc”, line 59, in draw
File “matplotlib\backends\backend_agg.pyc”, line 314, in draw
File “matplotlib\artist.pyc”, line 46, in draw_wrapper
File “matplotlib\figure.pyc”, line 773, in draw
File “matplotlib\artist.pyc”, line 46, in draw_wrapper
File “matplotlib\axes.pyc”, line 1701, in draw
File “matplotlib\artist.pyc”, line 46, in draw_wrapper
File “matplotlib\image.pyc”, line 237, in draw
File “matplotlib\image.pyc”, line 182, in make_image
File “matplotlib\cm.pyc”, line 167, in to_rgba
File “matplotlib\colors.pyc”, line 527, in call
MemoryError
Traceback (most recent call last):
File “cellprofiler\gui\cpfigure.pyc”, line 269, in on_paint
File “matplotlib\backends\backend_wxagg.pyc”, line 59, in draw
File “matplotlib\backends\backend_agg.pyc”, line 314, in draw
File “matplotlib\artist.pyc”, line 46, in draw_wrapper
File “matplotlib\figure.pyc”, line 773, in draw
File “matplotlib\artist.pyc”, line 46, in draw_wrapper
File “matplotlib\axes.pyc”, line 1701, in draw
File “matplotlib\artist.pyc”, line 46, in draw_wrapper
File “matplotlib\image.pyc”, line 237, in draw
File “matplotlib\image.pyc”, line 182, in make_image
File “matplotlib\cm.pyc”, line 167, in to_rgba
File “matplotlib\colors.pyc”, line 527, in call
MemoryError
Traceback (most recent call last):
File “cellprofiler\gui\cpfigure.pyc”, line 269, in on_paint
File “matplotlib\backends\backend_wxagg.pyc”, line 59, in draw
File “matplotlib\backends\backend_agg.pyc”, line 314, in draw
File “matplotlib\artist.pyc”, line 46, in draw_wrapper
File “matplotlib\figure.pyc”, line 773, in draw
File “matplotlib\artist.pyc”, line 46, in draw_wrapper
File “matplotlib\axes.pyc”, line 1701, in draw
File “matplotlib\artist.pyc”, line 46, in draw_wrapper
File “matplotlib\image.pyc”, line 237, in draw
File “matplotlib\image.pyc”, line 182, in make_image
File “matplotlib\cm.pyc”, line 167, in to_rgba
File “matplotlib\colors.pyc”, line 527, in call
MemoryError
Traceback (most recent call last):
File “cellprofiler\gui\cpfigure.pyc”, line 269, in on_paint
File “matplotlib\backends\backend_wxagg.pyc”, line 59, in draw
File “matplotlib\backends\backend_agg.pyc”, line 314, in draw
File “matplotlib\artist.pyc”, line 46, in draw_wrapper
File “matplotlib\figure.pyc”, line 773, in draw
File “matplotlib\artist.pyc”, line 46, in draw_wrapper
File “matplotlib\axes.pyc”, line 1701, in draw
File “matplotlib\artist.pyc”, line 46, in draw_wrapper
File “matplotlib\image.pyc”, line 237, in draw
File “matplotlib\image.pyc”, line 182, in make_image
File “matplotlib\cm.pyc”, line 167, in to_rgba
File “matplotlib\colors.pyc”, line 527, in call
MemoryError
Traceback (most recent call last):
File “cellprofiler\gui\cpfigure.pyc”, line 269, in on_paint
File “matplotlib\backends\backend_wxagg.pyc”, line 59, in draw
File “matplotlib\backends\backend_agg.pyc”, line 314, in draw
File “matplotlib\artist.pyc”, line 46, in draw_wrapper
File “matplotlib\figure.pyc”, line 773, in draw
File “matplotlib\artist.pyc”, line 46, in draw_wrapper
File “matplotlib\axes.pyc”, line 1701, in draw
File “matplotlib\artist.pyc”, line 46, in draw_wrapper
File “matplotlib\image.pyc”, line 237, in draw
File “matplotlib\image.pyc”, line 182, in make_image
File “matplotlib\cm.pyc”, line 167, in to_rgba
File “matplotlib\colors.pyc”, line 527, in call
MemoryError
Traceback (most recent call last):
File “cellprofiler\gui\cpfigure.pyc”, line 269, in on_paint
File “matplotlib\backends\backend_wxagg.pyc”, line 59, in draw
File “matplotlib\backends\backend_agg.pyc”, line 314, in draw
File “matplotlib\artist.pyc”, line 46, in draw_wrapper
File “matplotlib\figure.pyc”, line 773, in draw
File “matplotlib\artist.pyc”, line 46, in draw_wrapper
File “matplotlib\axes.pyc”, line 1701, in draw
File “matplotlib\artist.pyc”, line 46, in draw_wrapper
File “matplotlib\image.pyc”, line 237, in draw
File “matplotlib\image.pyc”, line 182, in make_image
File “matplotlib\cm.pyc”, line 167, in to_rgba
File “matplotlib\colors.pyc”, line 527, in call
MemoryError
Traceback (most recent call last):
File “cellprofiler\gui\cpfigure.pyc”, line 269, in on_paint
File “matplotlib\backends\backend_wxagg.pyc”, line 59, in draw
File “matplotlib\backends\backend_agg.pyc”, line 314, in draw
File “matplotlib\artist.pyc”, line 46, in draw_wrapper
File “matplotlib\figure.pyc”, line 773, in draw
File “matplotlib\artist.pyc”, line 46, in draw_wrapper
File “matplotlib\axes.pyc”, line 1701, in draw
File “matplotlib\artist.pyc”, line 46, in draw_wrapper
File “matplotlib\image.pyc”, line 237, in draw
File “matplotlib\image.pyc”, line 182, in make_image
File “matplotlib\cm.pyc”, line 167, in to_rgba
File “matplotlib\colors.pyc”, line 527, in call
MemoryError
Traceback (most recent call last):
File “cellprofiler\gui\cpfigure.pyc”, line 269, in on_paint
File “matplotlib\backends\backend_wxagg.pyc”, line 59, in draw
File “matplotlib\backends\backend_agg.pyc”, line 314, in draw
File “matplotlib\artist.pyc”, line 46, in draw_wrapper
File “matplotlib\figure.pyc”, line 773, in draw
File “matplotlib\artist.pyc”, line 46, in draw_wrapper
File “matplotlib\axes.pyc”, line 1701, in draw
File “matplotlib\artist.pyc”, line 46, in draw_wrapper
File “matplotlib\image.pyc”, line 237, in draw
File “matplotlib\image.pyc”, line 182, in make_image
File “matplotlib\cm.pyc”, line 167, in to_rgba
File “matplotlib\colors.pyc”, line 527, in call
MemoryError
Traceback (most recent call last):
File “cellprofiler\gui\cpfigure.pyc”, line 269, in on_paint
File “matplotlib\backends\backend_wxagg.pyc”, line 59, in draw
File “matplotlib\backends\backend_agg.pyc”, line 314, in draw
File “matplotlib\artist.pyc”, line 46, in draw_wrapper
File “matplotlib\figure.pyc”, line 773, in draw
File “matplotlib\artist.pyc”, line 46, in draw_wrapper
File “matplotlib\axes.pyc”, line 1701, in draw
File “matplotlib\artist.pyc”, line 46, in draw_wrapper
File “matplotlib\image.pyc”, line 237, in draw
File “matplotlib\image.pyc”, line 182, in make_image
File “matplotlib\cm.pyc”, line 167, in to_rgba
File “matplotlib\colors.pyc”, line 527, in call
MemoryError
Traceback (most recent call last):
File “cellprofiler\gui\cpfigure.pyc”, line 269, in on_paint
File “matplotlib\backends\backend_wxagg.pyc”, line 59, in draw
File “matplotlib\backends\backend_agg.pyc”, line 314, in draw
File “matplotlib\artist.pyc”, line 46, in draw_wrapper
File “matplotlib\figure.pyc”, line 773, in draw
File “matplotlib\artist.pyc”, line 46, in draw_wrapper
File “matplotlib\axes.pyc”, line 1701, in draw
File “matplotlib\artist.pyc”, line 46, in draw_wrapper
File “matplotlib\image.pyc”, line 237, in draw
File “matplotlib\image.pyc”, line 182, in make_image
File “matplotlib\cm.pyc”, line 167, in to_rgba
File “matplotlib\colors.pyc”, line 527, in call
MemoryError

Hi Dita,

How big are your images (i.e, pixel dimensions), if I may ask?

Regards,
-Mark

2802 by 2804 pixels (23Mb TIF files)

Still couldn’t open the original tif image on my much faster newer work computer. I reduced the pixel dimensions dramatically (884 by 883 pixels) and was able to open it, so I guess I am just outrunning the memory. Unfortunately this lower resolution wipes out all the interesting features. I will read your faq on memory usage and consult with my local friendly IT people, but any specific advice on how to maximize my pixel input without paralyzing my computer would be appreciated.

I don’t know if you have access to a 64-bit machine, but that’s one easy way to get a boost in memory usage.

Could you send us an example of one of your files so we could take a look? It’s too big for an upload to the forum but could try post it to [urlpicasaweb.google.com/]Picasa, use YouSendIt, or upload to our FTP server here. If you choose the 3rd options, post here and I’ll walk you though the process.

Regards,
-Mark

could you please post the ftp instructions?

i have uploaded an example file