Comments (4)
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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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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need to decide which stats to choose, currently: skew, compact, footprint
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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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Related Issues (20)
- Tiff ValueError: the total number of frames should be at least 50. RAW to TIFF conversion in Fiji HOT 2
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- Bug: Merge ROIs duplicates
- FEATURE: operating extraction on cropped region HOT 2
- Deconvolution for RGECO neuronal signal
- BUG: error in anatomical detection using cellpose 3 HOT 1
- BUG: error when running suite2p HOT 2
- Don't show ROIS in main screen HOT 3
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- BUG: sbx_to_binary computes nframes incorrectly with multiple channels if longer than batch_size frames HOT 1
- DOC: some readthedocs.io links to API are broken
- BUG: Can not handle an h5 file with 5D data structure HOT 3
- BUG: Partial analysis on subset of data does not work
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- FEATURE: ROI registration and interpretation of
- Imaging with Fluo-4
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