I’m new to CP and imaging analysis in general, so bear with me.
My goal is to quantify different types of macrophages (different stains) on an image, but I’m hoping to use the original .ND2 file or a four channel .tiff file. However, regardless of how I save these images, CellProfiler isn’t recognizing the channels that should be in the image’s metadata.
Just to provide more context, I’m looking at an image that has four channels resulting from the different stains used (DAPI (blue), CY5 (orange), etc.).
When I upload the images to ImageJ, I can see the correct channels. However, when I try to convert the image to grayscale, CP seems to only recognize RGB and Alpha channels. Is this to be expected? Does anyone have any suggestions?