Code for quantifying cell counts for whole brain lighsheet imaging. This repository assumes that we have the cell locations in an XML and the image transformations from the CCF alignment. Please, refer to these repositories to be able to generate these results:
generated from AllenNeuralDynamics/aind-capsule-template
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Takes the output of segmentation and ccf registration to calculate cell counts per brain region
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AllenNeuralDynamics/aind-smartspim-quantification
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Takes the output of segmentation and ccf registration to calculate cell counts per brain region
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