We are trying to determine whether qupath can be used for a specific type of image analysis. We wanted to reach out to see if any users of this forum had any recommendations. Below is a brief description of the analysis. We will attach an example image at the bottom of the post. Thanks in advance for any help you can provide!
All images scan the Z-plane of a neuron. Each image contains 20-40 z-slices and 4 different channels. Channels 1,2,4 represent different fluorescently labelled RNA molecules. Channel 3 shows an antibody labeling for a neuronal marker, which provides a visual of the cell body. All images are 8 bit, gray-scale and captured with a fluorescent microscope.
Ultimately, we would like to calculate the number of fluorescently labeled RNA molecules (sometime referred to a puncta) present within the neuron. This can be done in FIJI by first determining the location of the cell body within the channel 3 and creating a ROI. We then select an appropriate threshold for the images. The ROI and the threshold are then applied to channels 1,2, and 4. Finally, we run the “analyze particles” function to quantify the number of molecules present within the ROI in channels 1, 2, and 4. However given the number of images within our data set, we are interested whether this process could be augment/automated using qupath or another program listed on this forum (if we are looking in the wrong place, any direction would be appreciated).
There are a few posts that deal with somewhat similar challenges related to analyzing images that contain RNA molecules, here and here, among several others. These post suggest that qupath may be a good fit for what we are trying to do. Again, thanks for any help.
Below is an example image with channels split: