In the Target EGFP experiments, what projection is the data quantifying? Is it the EGFP coming from the rAAV injected region? If so, is there a way to programmatically access the levels of tdTomato from the CAV injection? In other words, is the retrograde tdTomato level per brain region also located somewhere in the atlas or in the SDK? Thanks very much
Hello, would you mind sharing an experiment ID or link to the experiment you are referring to?
Hi! Thanks for responding. One example would be something like experiment 569993539, where there are two viruses injected in two different channels (green = rAAV into MOs, red = CAV-cre into SSp-bfd). In this setup, I’m not sure what the projection volume is quantifying – is it the red signal that represents all of the retrogradely labeled regions that project to SSp-bfd? Or is it the green that represents all of the MOs neurons that project to SSp-bfd? If its the latter (i.e. the green axons are quantified), is there an ability to access only the red signal?
Hi This experiment and other similar tracing experiments in Ai75 were used in the paper Regional, Layer, and Cell-Type-Specific Connectivity of the Mouse Default Mode Network (https://www.sciencedirect.com/science/article/pii/S0896627320308898?via%3Dihub#mmc5).
Green signal represents projection from cells retrogradely labeled by CAV-Cre.
In the experiment 569993539, we have the projection volume quantifying green signal from the MOs cells retrogradely labeled by CAV-Cre injected in SSp-bfd. But we do not have the quantification for red signal.
Thanks so much. Is there any way that the Allen can go back and obtain quantification of the red signal for each Ai75 injection? It would be incredibly useful.
Just following up on this – the retrograde label in the Ai75 injections is incredibly useful data. Our experiments right now are trying to identify loop structures in the brain. Having simultaneous readouts of retrograde and anterograde values in these experiments would be extremely useful for us. Is there any way we can get the red levels in each brain region?