Hi @roberrttt,
This is a lot of broad questions, but I’ll take a shot at a few of them. Given the other community forum post you mention, I’m going to assume you are interested in the original Allen Mouse Brain Atlas, but I’d also encourage you to explore the more recent single cell and spatial data available on the Allen Brain Cell Atlas.
What is the best approach to efficiently access and download the gene expression datasets for specific cortical regions? Are there any recommended tools or scripts that can streamline this process? ← I’d recommend using the API. In addition to the community forum post you mentioned, there is additional documentation here.
(I don’t have an answer for your second question… maybe other folks do?)
What are some recommended tools or software for creating visual representations of these data? ← There are many tools for this! Some of the ones for visualizing the CCF in this list could also be used for gene expression, likewise for generender and cocoframer (mentioned in the other forum post). The Allen Institute also has a downloadable software for 3D viewing, but note that this is no longer officially supported.
any tips on interpreting these visualizations in the context of neurodevelopmental research ← I’d suggest you look at the Allen Developing Mouse Brain Atlas, if you haven’t yet. This will let you know how expression for ~2000 genes change across mouse development.
tutorials; documentation; or case studies related to the use of the Allen Brain Atlas ← All the official documentation is here. We also have a YouTube page, and here is a reasonable search to get you started.
As for challenges, pitfalls, and any other bits I may have missed, I’ll leave that to others.
Best of luck,
Jeremy