Nucleus classification

Hi,
The goal is to separate nuclei into 3 category: small, normal and big nucleus depending on size and further want to add by circularity (ex. dead cells usually more round).
Thought it would be relatively easy to do with CP but receiving an error.
Here is the error code that I am receiving.

Traceback (most recent call last):
File “cellprofiler\pipeline.pyc”, line 309, in run
File “cellprofiler\modules\saveimages.pyc”, line 445, in run
File “cellprofiler\modules\saveimages.pyc”, line 489, in run_image
File “cellprofiler\modules\saveimages.pyc”, line 899, in save_image
File “cellprofiler\modules\saveimages.pyc”, line 1001, in get_filename
File “cellprofiler\measurements.pyc”, line 351, in get_current_image_measurement
File “cellprofiler\measurements.pyc”, line 358, in get_current_measurement
File “cellprofiler\measurements.pyc”, line 377, in get_all_measurements
AssertionError: No measurements for Image.PathName_OrigBlue

Info about files, 3 *.tiff files are single channel but 3 images in stack which I need to do maximum projection and a pipeline file.

Thank you,
Aidos






test setup nuclei analysis v2.cp (12.2 KB)

Hi Aidos,

If you uncheck the “Create subfolders in the output folder” setting in SaveImages, the pipeline should work. Also, since the projection is only completed after all the images are loaded, you should select “Last cycle” for the “Select how often to save” setting in SaveImages as well.

Regards,
-Mark

Hi Mark,

Weird, now there is no errors but the Excel files are empty,only headers there.

Regards,
Aidos

Hi Aidos,

The reason for this is the IdentifyPrimaryObjects modules did not detect any objects; with no objects, nothing is written to the per-object spreadsheets. It appears that you are passing the output image from ApplyThreshold to these modules, and ApplyThreshold is producing a blank image. So you may want to check/adjust the settings in ApplyThreshold.

Indeed, ApplyThreshold isn’t really needed in the pipeline at all, since IdentifyPrimaryObjects serves the same function while also producing the objects needed for measurements.

Regards,
-Mark

Hi Mark,

Thank you it works.

Regards,
Aidos