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I have recently started imaging the Dorsal Root Ganglia in which the primary sensory afferents reside. My problem arises from the huge variation in cell body size of these cells in which the largest neurons are >30um in diameter and the smallest are ~10um in diameter. The below image is from a single plane of a 2p recording showing the large variation with a range of around 2-3 fold. I have been messing with gsig and merge_thr to try and find an optimal balance but it feels like a push and pull that I can't get right. e.g. The small cells get merged together with too large of a gsig and so I increase the merge_thr, but then it starts to break up the large cells into 2 pieces. I've done a fair bit of hyperparamter searching and haven't found one I particularly like.
Not sure if there is an optimal solution, but I am not well versed in exactly how CNMF works know how restrictive gsig is to finding cells.
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I have recently started imaging the Dorsal Root Ganglia in which the primary sensory afferents reside. My problem arises from the huge variation in cell body size of these cells in which the largest neurons are >30um in diameter and the smallest are ~10um in diameter. The below image is from a single plane of a 2p recording showing the large variation with a range of around 2-3 fold. I have been messing with gsig and merge_thr to try and find an optimal balance but it feels like a push and pull that I can't get right. e.g. The small cells get merged together with too large of a gsig and so I increase the merge_thr, but then it starts to break up the large cells into 2 pieces. I've done a fair bit of hyperparamter searching and haven't found one I particularly like.
Not sure if there is an optimal solution, but I am not well versed in exactly how CNMF works know how restrictive gsig is to finding cells.
Thanks!
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