3D area around detected cells // own region of interest?

[jkaiser87]

Thank you so much for this amazing tool, it works very well in our hands, even on P14 brains!
I was wondering whether you had any ideas on how to implement these 2 following ideas:

• 3D area around the detected cells: Would it be possible to create a 3D bound area around the detected cells to better compare between different animals? In our hands, we often don't evaluate every slice per brain (to keep some wells for additional stainings), so for comparing different animals, the cells might be traced on slightly different levels, which might not be easy to compare. Additionally, our goal is to in the end compare different animals in different groups, is it possible to combine the tracings of different animals?

• create own region of interest for counting cells: Is it possible to create my own region of interest to get numbers per cell in e.g. the lateral cortex vs. medial cortex rather than using the Allen brain atlas annotations?

I would highly appreciate any input into these two ideas,

thanks and best,
Julia