Implement decoding project

[fkloosterman]

Migrated from Bitbucket

• Original Author: @MarineChap
• Original Created: March 21, 2022 at 11:22 AM UTC
• Original URL: https://bitbucket.org/kloostermannerflab/falcon-core/issues/67/implement-decoding-project
• Kind: proposal
• Priority: major

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@fkloosterman

Extensions concerned :

• falcon-fklab-extensions (public/test-decoding branch)
• falcon-decoding-extensions (private/test-decoding branch)
• falcon-behavior-extensions (private/speed_threshold_processor branch)

External lib concerned :

• py-compressed-kde repo (public / utilities_for_decoding)

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Graph architecture (March 2022):

Neuropixels input block (grey) :

• Update the open-ephys reader for new oe version + speed optimized based on the new data format order : PR to review (need the PR upper to be merged first)

• Switch column/sample in the column / timeseries datatype + add expand option in number of samples: PR to review and merge ⚠️

  • About this PR :

    • Be careful to the speed since changing the format (change in the multichannelfilter and in the openephys reader for example)
    • Be careful when requesting a new slot from the ring buffer without resetting the packet - if it was an expandable one, it will keep the size of the packet the last time the slot was used

• TTLsink processor PR to review ⚠️

• Spatial Filter : PR to review and discuss - Transform for a linear global filter (no spatial implementation per-se) ❌

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Decoding Pre-processing pipeline:

• Distributor ✅
• Spike Feature processor: PR to review and merge (wait for the utilities_decoding merge) ✅
• implement the datastream name added in falcon-core: PR merged ✅

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Decoding pipeline :

• Add methods in the py-compressed-kde used by the online_decoder processor : PR to review and merge⚠️
• Add OnlineDecoder and MultiLikelihood processor: PR to merge (wait for the py_compressed kde method) ✅
• Add ReplayIdentifier processor : issue to discuss / PR to review

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Encoding pipeline :

• Bug to fix in the share state system to be able to share pointer of the decoder object : PR merged ✅
• EncodingFeature processor : PR to review ⚠️
• OnlineEncoding processor : PR to review ⚠️

Behavior pipeline:

• speed threshold detector : PR to review - smoother to improve

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Validation :

For online decoding validation: see in the fk-fileserver/Marine/online_decoding_test folder

• Data folder contained everything to be able to run an offline encoding with dashboard + online decoding with Falcon
• See ReadMe for instructions on how to set up the environment

**For latency validation: (**See slides) ⚠️

[fkloosterman]

Description edited by @MarineChap on March 21, 2022 at 11:37 AM UTC

[fkloosterman]

Description edited by @MarineChap on March 21, 2022 at 12:46 PM UTC

[fkloosterman]

Description edited by @MarineChap on July 26, 2022 at 01:36 PM UTC

[fkloosterman]

Description edited by @MarineChap on September 09, 2022 at 10:51 AM UTC

[fkloosterman]

Description edited by @MarineChap on September 29, 2022 at 10:09 AM UTC

[fkloosterman]

Description edited by @MarineChap on September 29, 2022 at 12:32 PM UTC

[fkloosterman]

Description edited by @MarineChap on December 20, 2022 at 04:05 PM UTC