Issue with SaveImages after applying DisplayDataOnImage

When I use DisplayDataOnImage and then try to save the image with SaveImages, about 25% of the top and right side of the image gets cropped off in the saved file. The base images or images with just outlines overlayed save correctly with SaveImages. The images with displayed data also appear fine in the CellProfiler window and save correctly when manually saving them to a pdf via the window file menu.

Rachel

Thanks for reporting this. We’ll add it to the known bugs list. As you point out, a workaround for now would be to manually save as pdf.

This should only affect DefineGrid, TrackObjects, and DisplayData on image. Other images should save correctly.

The fix for the issue will be available in the next release of CellProfiler.

We’ve just made a new release, r10415. Does it fix this problem?
-Mark

Hello,

the fix you reported for 10415 worked, but the problem is back with version 11710. This time DisplayDataOnImage passes a completely blank picture to pipeline. It can be manually saved just fine, but if passed on for further processing in the pipeline (i.e. resize or save), the image is blank.
Bye,
Marc

Hi Marc,

I’m not able to replicate the problem you report, as such. Using a modified version of the ExampleHT29 pipeline (attached), I get the following output (see below).

However, this was the case if I saved as PNG or 8-bit TIF. Oddly, if I saved as 16-bit TIF, my default freeware viewer (IrfanView) identified it as a 2-frame TIF in which the 2nd frame was blank. Does this even remotely sound like what you encountered?

EDIT: Also, are you using Mac or Windows? Another user just posted something similar, and I wonder if it’s the same issue in play (I use Windows 7).

Regards,
-Mark


ExampleHT29.cp (12.1 KB)

Hi Mark,

I am indeed a Mac user. After your reply, I repeated the save and had no more problem on my workstation. But on my Mac laptop, the problem persists and is exactly what the other user reported. In my case both computers are using the same pipeline and the same dataset, so this is very strange. One difference is that on my laptop, the data is on the desktop, so it might also be a permission problem. I’ll try that and keep you posted.
I have never tried saving as a 16-bit TIF, so I can’t answer your question.
Bye,
Marc

Hi Mark,

the problem persist, even when the images are in my home folder. As I said it is not a consistent problem, so I guess hunting down the reason will be impossible. I’ll try to download another copy of the app and try again.
Bye,
Marc

Hi Marc,

Just re-visiting this issue: Did re-downloading the app solve the issue, or is it still a problem?

Regards,
-Mark

Hi Mark,

it is working fine now, I have no idea what was going on when it didn’t. This was very useful since I had to train manually a machine learning tool in KNIME and I needed to label the nuclei. The reason why I had to do that is that the tool for exporting to database still does not work. I therefore couldn’t use CPAnalyst in conjunction with our cluster.
Thanks,
Marc

I seem to be having the same problem: after using DisplayDataOnImage, png files saved with SaveImage come out completely white. In response to Mark’s earlier post, I’ve also tried to save them as 8 and 16 bit TIF images; these have also been blank (not only in my default preview image program but also in photoshop, etc.). As was previously reported, the base image or image with outlines saves correctly. The DataOnImage displays correctly in the CellProfiler window and can be saved manually. I am using a Mac laptop, and have tried reinstalling CellProfiler, but this issue was not resolved.

It sounds like there might not currently be a solution to this issue, but if there is - I would appreciate the help! Any other thoughts on how to export the images without doing so manually would also be great. I’ve attached the pipeline I am using and an example image. Thank you very much in advance,

Rachel



Adipocyte Pipeline numbered Rodeheffer Lab Modified for GFP.cp (14.2 KB)

Hi,

@Rachel: I think this is probably the same Mac bug that is discussed in this Forum thread. As Mark says there, our suggested workaround is to upgrade your CP to the 2.0 “bugfix” version (not 2.1). Please note the caveats!
github.com/CellProfiler/CellPro … TrunkBuild
Note that on my Mac with OS 10.8 and CP release version 11710, I don’t see this saved images issue, so it is for some unknown reason hit-or-miss.
Another workaround is to use a Windows computer in which we haven’t seen this problem to my knowledge.

@MarcKobudo: Sorry, just noticed the database issue you mentioned – are you still having trouble, and is the trouble in CP or KNIME?

Best,
David