CellProfiler with tile images

Hi everybody,

I am trying to perform image analysis with tile images (10x, 9 fields) from immunofluorescence experiments.

Basically we using the dapi signal to detect the nuclei and we quantify the red and green signals corresponding to two different antibodies. We are using this with single field images 40x with no problem.

However I have problems first with metadata, it seems that several images are detected as you can see here.

Thanks in advance for any tips



Hi Cyril,
The “Series” are different, so it seems these are different images. Did you have z-stack?
You can upload your pipeline, some images, and name of each channel for us to take a look.

Thanks for your answer Nasim. We are not supposed to have z-stacks. I uploaded the pipeline. I tried to upload one image but the .czi is not authorized. Which format should I use ? 2017_V2_intensity_filterEdu_EdU_PCNA.cpproj (15.1 MB)

Hi Cyril,

You can compress files into a .zip folder to upload them.

Some microscope hardware will save multiple images in the same file as if they were z-planes. It looks like each series in your image is a different size. Was this an image of a tissue section? Some microscopes pack in several scaled-down versions of an image to aid in displaying a preview, if this is the case you’ll probably just want to analyse a single set from each file. You can restrict this in the NamesAndTypes module.

Thanks for your answer. No it’s not a tissue section therefore I don’t understand why I have several images of different sizes… I’ll check how to restrict this.

Image is too big to direct upload, here’s a link to download it.

Thanks for your help.

From the pixel values I’m pretty sure these .czi files must be pyramidal where different resolutions are saved for an image.

Your pixels values are always half of the others. I can’t download your files right now but if you try and open them in FIJI then Bio-Formats should pick up the different resolution levels.

To move forward you could just filter out the images to select only the full res image.

Yup, it’s just different resolutions of the original tiled image. The easiest solution to this would be to add the condition “Metadata --> Series --> Is Equal To --> 0” into your NamesAndTypes image definitions.

Thanks for your answer, I see the problem now. However I don’t find where I can filter the highest rez images (I can’t find what you wrote, I’m using v3.1.9)

Metadata --> Series --> Is Equal To --> 0” into your NamesAndTypes image definitions.


an option would be to use czireader_complete and read only the pyramid level with the full resolution and use the results in CP.

Are you assigning a name to “Images Matching Rules” in the NamesAndTypes module? Activating this setting should make the conditions dialog appear.