Help

cellprofiler

#1

hey,

this is my first time using a cell image analysis software. its a cool software but i have a lot of questions (some of them are silly). I am having some trouble loading a video clip. I looked at the example online about tracking objects. Im using the same pipeline as the example, but i keep getting this error:
" There was a problem running the analysis module LoadImages which is number 01.
Image processing was canceled in the LoadImages module because there are no image files with the text “DAPI” in the chosen directory (or subdirectories, if you requested them to be analyzed as well)."

The .avi file i am using has 25 frames/second but the one in the example online was only 7 frames/second.
is that the reason my video clip isnt work?
any idea why i’m getting this error?
i feel like i am missing something but i cant figure out what. thank you for the help.


#2

Hi,

The LoadImages module is looking for image files with the word ‘DAPI’ in the name. If you change ‘DAPI’ to match how your files are named (for example, if they are named Image01, Image02, Image03, you would want to look for ‘Image’ in the name), it should work.


#3

hey.

thanks for the help. I have another question.
I want to save the images produced from the MeasureObjectNeighbor module and the SaveImage module isnt letting me do that. the MeasureObjectNeighbor module produces 4 images that are put in boxes next each other and I need to save the cells colored by number of neighbors image for every cycle. is there a way for me to save the image produced by the module without having me save the images individually for every cycle. There are 169 cycles and id rather not be clicking the save button for every single image.

thanks!
Niketa


#4

Hi Niketa,

You can save the image of the number of neighbors by specifying that setting in the MeasureObjectNeighbors module, and then SaveImages (if you haven’t already, take a look at the “Tissue Neighbors” pipeline on our example pipeline page). One additional step is if you want to save a unique file of the same image for each cycle, one way to do this to specify “N” for the “Enter text or metadata tokens…” in SaveImages.

Regards,
-Mark


#5

hey,

so i tired what you told me friday and it still hasnt worked. I am not being able to attach the pipeline i’m using because it keeps telling me ‘sorry the board attachment quota has been reached’. But here is the pipeline i’m using:
LoadImages
GroupMovieFrames
ColorToGray
ImageMath
IdentifyPrimAutomatic
OverlayOutlines
MeasureObjectNeighbors
MeasureObjectAreaShape
MeasureObjectIntensity
ConvertToImage
SaveImages
ExportToExcel
SpeedUpCellProfiler

this is the image that cell profiler is saving for every cycle: img695.imageshack.us/img695/7334 … 624004.png
this is the one that i want it to save for every cycle: img59.imageshack.us/img59/606/ce … berofn.png

also i keep getting this error: "the images you have loaded in the SaveImages module are outside the 0-1 range, and you maybe losing data. Note, however that IlluminationFunctions are often in the range 1 to inf, and in this case the warning can be ignored’.
maybe this has something to do with cell profiler not saving the image i want.

thanks for the help!
Niketa


#6

Hi Niketa,

To save an entire figure, you must specify the module number in first setting in the the SaveImages module (select “Other” and type the number), and specify ‘fig’ as the format to save as. However, if you use this method, there are a few caveats:

  • You must keep the module window open during the run so it can save the figure.

  • It will save the entire figure, so some cropping will be necessary after the fact to extract the subplot that you want.

  • It will produce a .fig file that is only openable in MATLAB.

Unfortunately, there is no way to automatically save just a module subplot (as opposed to an image produced directly by the pipeline) during an analysis run.

The message you are getting is just a warning, rather than an error. In your case, it’s not something to worry about.
Regards,
-Mark