Saving images

cellprofiler

#1

Hi,

I am using the module MeasureImageAreaOccupied and I would like to save the images/figures obtained with this module. I tried the SaveImage module but it seems I cannot choose the image created by this module. If someone knows how I could save those images, your help would be appreciated.

thank you,
Daniel


#2

Hi,
This is a great question. By using the MeasureImageAreaOccupied module, the measurement is saved as an object. You will need to add the ConvertToImage module (in the Object Processing category) before the SaveImages module. In the ConvertToImage module, select the name of the object identified in MeasureImageAreaOccupied and select the remaining settings. Then, in the SaveImages module, you can select the new name from the ConvertToImage module and save it.

~martha


#3

Hi Martha,

Thank you for your answer.
I added the ConvertToImage module in my pipeline but I cannot select anything in the first field for the object name. The scrolldown menu is in grey and I cannot even click on the arrow to select a name. I tried to give a new name to the object in my MeasureImageAreaOccupied with no success. I also tried to run it without selecting anything and it didn’t worked (not surprising). I am using the latest version v1.0.4884.
Am I doing something wrong or do I forgot to do something ?

thank you again,
Daniel


#4

Hi,
Do anyone knows how I could solve the problem I have with the ConvertToImage module I described in the previous post.

thanks
Daniel


#5

Hmm, it looks like MeasureImageAreaOccupied doesn’t add the second field to the objectgroup. This would allow e.g. ConvertToImage to see your object in its popup list.

I will fix this bug, but until our next recompile and release, you could try this workaround:
(1) setup IdentifyPrimAutomatic with similar settings to your MeasureImageAreaOccupied and then follow this with MeasureObjectAreaShape.
(2) Multiply the number of identified objects in IdentifyPrimAutomatic by the first feature (mean Area) from MeasureObjectAreaShape. This should give you essentially the same value as you would get from MeasureImageAreaOccupied.

Hope this helps,
Dave


#6

Thanks for your answer Dave,

I will probably have to wait the new version.
I am using MeasureImageAreaOccupied in a wound healing assay and I measure the area of a “smoothed” image. I tried the steps you told me anyway, but it doesn’t works for this.

thank you for your help,
Daniel


#7

Hi,
We will be re-releasing CellProfiler in the near future. The error that you reported will be fixed, along with a few others. Please check back on the CellProfiler.org web page to see if the new release has been posted.


#8

Hi,
A new version of CellProfiler has been released. V.1.0.4942 will fix this issue!
martha


#9

Hi,

Just a couple of technical notes for the record:

(1) I called this a “bug” earlier, but generally we don’t save images from Measure Modules, except for special cases like this, so let’s just call this an “upgrade” :smile:
(2) The image will be added to the imagegroup (rather than the objectgroup, which I stated earlier). Thus, a module like SaveImages will see the MeasureImageAreaOccupied thresholded image automatically

Cheers,
Dave


#10

Thank you all for your help !
It’s really appreciated.

Daniel