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marius10p avatar marius10p commented on May 30, 2024

Trying to use Allen datasets for this, one for each CRE line, except EMX for which we will use several (it's a dense label). Should consider adding neurofinder datasets, which are very different because they are short and more noisy.

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marius10p avatar marius10p commented on May 30, 2024

Allen datasets are noisy for most CRE lines and include weird pre-processing steps like pixel deconvolution. Will only use some of their EMX-CRE. Investigating the neurofinder datasets now. Also asking Mario for some of his 2x zoom data.

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carsen-stringer avatar carsen-stringer commented on May 30, 2024

need to decide which stats to choose, currently: skew, compact, footprint

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marius10p avatar marius10p commented on May 30, 2024

Added normalized pixel count as statistic. Default classifier includes a single mesoscope recording with ~6,000 cells and ~6,000 non-cells at low zoom and 2:3 aspect ratio. The trained data was before we brought back connected regions, so some of the non-cells are scattered. Classifier histogram smoothing works as before except the grids are determined from the training data as quantiles rather than pre-defined.

No other statistic helped performance on test data. We tried aspect_ratio, std, kurtosis, mean image correlation, and correlation with neuropil.

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