Data handler cortexlab

• Data handler connects to correct alyx database on cortexlab

Improve EphysPostDLC

• Fixes to EphysPostDLC
• Small change to storing in dsp.voltage.decompress_destripe_cbin function

Task queue fix

• Small fixes to local server task queues

Minor changes spikeglx, dlc_qc_plot, atlas regions

• Authenticate alyx user in Task class
• Some fixes to make dlc_qc_plot in EphysPostDLC more reliable
• SpikeGlx:
  • supports reading of flat binary files without meta data
• atlas.Regions:
  • add support for region ordering in BrainRegions object
  • bugfix in transposing of RGB image data for coronal slice plots
• voltage: decompress cbin
  • add support for custom spikeglx.Reader

2.9.1

What's Changed

• deprecation warnings and documentation for spike sorting loading method
• bugfix: remove lru_cache on AllenAtlas class for iblviewer

EphysDLC task run on local servers

• Adding EphysDLC task in ephys_preprocessing pipeline
• NOTE: requires DLC environment to be set up on local servers!
• Fixes to EphysPostDLC dlc_qc_plot

QC Snapshots and SpikeSortingLoader

Release Notes 2.8.0 2022-01-19

• Add lfp, aprms, spike raster and behaviour report plots to task infastructure
• Computation of apRMS in decompress_destripe_cbin before conversion to normalised units
• Add SpikeSortingLoader class in brainbox.io.one

EphysPostDLC fixes

• Fixes and better logging for EphysPostDLC task

Report Snapshots

• New ReportSnapshot class
• DLC QC plots, as part of EphysPostDLC task
• BadChannelsAP plots for ephys QC
• Fix typo in camera extractor

Spike sorting updates and snapshot class

• Snapshot class to register images as notes in Alyx
• Ephys pipeline: RawEphysQC: outputs channels labels as part of pipeline
• Ephys pipeline: spike sorting
  • dsp.voltage: destripe detects bad channels and interpolate them
  • synchronisation 3B: gives a 10% leeway to throw exception
  • spikes sorting task outputs the RMS plot