I am a grad student and I have been struggling to correctly use the Reference Space API with the Coronal Atlas of the P56 Mouse Nissl Stains dataset. I have been working with the ‘reference_space.ipynb’ file that is provided as an example to try download only substructures of the atlas (e.g. Isocortex or Primary Motor Cortex, link to file: http://alleninstitute.github.io/AllenSDK/_static/examples/nb/reference_space.html).
The reference files seem like they are structured in a way that all three of the atlases for Atlas ID 602630314 (3D coronal average template), 1 (Coronal), 2 (Sagittal) are all grouped into the same reference space (indicated by 1 in this case). I have only been able to download a 10x and 100x downsampled reference atlas for the 3D coronal atlas. My first question is if there is a way to get the full resolution of the reference atlases in the reference space (seems to be only 10, 25, 50, 100 micron resolution options which are all downsampled when the true resolution is 8K by 11.4K images)?
From the documentation of the API, it seems like I need to know the name of the nrrd file corresponding to the atlases for the dataset of Atlas ID 1 (potentially something like P56_Mouse_annotation_XX.nrrd where ‘XX’ might be the micron resolution). I have found a document about the 3D atlas release (http://download.alleninstitute.org/informatics-archive/october-2014/mouse_expression/Accessing_October_2014_expression_data.pdf) but have had no luck trying to import the file into a ipython environment. I am able to download all of the nissl images and full atlas images in jpg form but I am interested in only a subsection of the atlases (and potentially and easy way to navigate between different structures in python). My next best alternative would be to use the atlases as a stencil for the intended ROIs but hopefully there is a better solution!
Thank you for your time and help in this matter. I look forward to your response!