LoadImages string help

Hi,

I am a relative novice to CellProfiler and currently managing to work my way around OK but I have a query about loading groups of images. I was wondering whether someone might be able to give me a few pointers?

I have a set of images that follow the pattern below:

A1–W000001–P000001–Z000000–T000000–DAPI.tif
A1–W000001–P000001–Z000000–T000000–FITC.tif
A1–W000001–P000001–Z000000–T000000–TxRd.tif
A1–W000001–P000002–Z000000–T000000–DAPI.tif
A1–W000001–P000002–Z000000–T000000–FITC.tif
A1–W000001–P000002–Z000000–T000000–TxRd.tif
A2–W000002–P000001–Z000000–T000000–DAPI.tif
A2–W000002–P000001–Z000000–T000000–FITC.tif
A2–W000002–P000001–Z000000–T000000–TxRd.tif

I have tried to load the images using the LoadImages module with the following settings:

file type to be loaded= individual images
file selection method=order
number of images in each group?=3

then 3 images,

the position of this image in each group= 1, 2 or 3 respectively

and

name this loaded image = DAPI, FITC or TxRd respectively.

However I cannot get the images to load. Any help will be much appreciated.

Cheers,

Ian

Hi Ian,

Can you clarify what you mean by this? Are you getting an error message or something else?

Regards,
-Mark

Hi Mark,

Apologies for any confusion.

I think I now know where I went wrong originally, however I have still not solved the problem. Originally I put either “DAPI”, “FITC” or “TxRd” into the “Position of this image in each group” box. The box was then highlighted red and a stop sign appeared next to the module in test mode. I am now putting “1”, “2” or “3” into the aforementioned box and it is allowing me to continue, as below:

However it now appears that it is only loading the 1st three images in my list and not the subsequent images, as seen in the screencap below:

Thanks for you help,

Ian

Hi Ian,

What you are seeing is the correct behavior. CellProfiler processes the images in successive cycles, using each set of images you’ve defined for each cycle. In your case, you have defined the DAPI, FITC and TxRed images as comprising an image set, and the LoadImages display is showing that it’s loading the P000001 set to process as the first cycle (which I assume is correct?). The second cycle, it will load the P000002 DAPI, FITC and TxRed images, and so on.

In Test mode, you can examine one cycle at a time, which is why it is showing the first set in the screenshot of LoadImages. You can jump ahead to further sets using the “Next image” button or the “Test mode” menu item.

I should mention that it is typical in CellProfiler to use a text pattern to define the image sets. I wold recommend setting the file selection method as “Text-Exact match” and the “Text that these images have in common” as “DAPI” for one, “FITC” for the 2nd, and “TxRed” for the third, and leave it to CellProfiler to match the images up and deal with the ordering. However, since the “Order” method works, you can leave it as-is.

Cheers,
-Mark

Thanks very much for your help Mark. That’s great.

Ian