This may be a somewhat niche issue, but still looking to see if you can provide some insight. I am using the quint pipeline to register my stained sections and then Ilastik pixel classifier+ object classifier to segment a plasticity marker. I get the xy coordinate of each instance of this marker, and then want to map it back onto my registered sections to get subregion information. The goal is whole brain analysis of my marker, so i care about the z coordinate position of each subregion, as they can shift based on human error and such. I used a script to extract the average z position of each region from the json file of each image. My issue arises here, where some regions do not appear to be labeled in the json file, despite the csv generated having objects within those regions. for example the retrosplenial area, one of my ROI will show up in my object report but not be named in the json file, leaving me unable to get the z position for these objects/the average for the region. I did come across the box below when looking into the documentation, and thought that this could be the source of my issue:
Does this mean that using a custom xlsx file could solve the issue described above?
Sorry if my question is somewhat confusing, and I can provide more context/data examples if needed.
Thanks!
Jacob
This may be a somewhat niche issue, but still looking to see if you can provide some insight. I am using the quint pipeline to register my stained sections and then Ilastik pixel classifier+ object classifier to segment a plasticity marker. I get the xy coordinate of each instance of this marker, and then want to map it back onto my registered sections to get subregion information. The goal is whole brain analysis of my marker, so i care about the z coordinate position of each subregion, as they can shift based on human error and such. I used a script to extract the average z position of each region from the json file of each image. My issue arises here, where some regions do not appear to be labeled in the json file, despite the csv generated having objects within those regions. for example the retrosplenial area, one of my ROI will show up in my object report but not be named in the json file, leaving me unable to get the z position for these objects/the average for the region. I did come across the box below when looking into the documentation, and thought that this could be the source of my issue:
Does this mean that using a custom xlsx file could solve the issue described above?
Sorry if my question is somewhat confusing, and I can provide more context/data examples if needed.
Thanks!
Jacob