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release_notes.md

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Release Notes 1.4.13 - 2020-02-07

  • Hotfix: rig transfer - create probes. One variable used before assignation.

Release Notes 1.4.12 - 2020-02-06

  • ONE.load overwrites local file if filesizes different or hash mismatch
  • ephys extraction:
    • registration sets the session.procedure field to acute recording
    • bugfix synchronization on re-extraction: always recompute spike.times from spike.samples
    • ephys registration sets the session.procedure field to acute recording
  • training extraction:
    • added biasedVisOffChoiceWorld as training extractor
  • wheel data
    • dropping support for wheel velocity, not extracted anymore

Release Notes 1.4.11 - 2020-02-14

  • bugfix: Include sessions data files for ephys mock
  • bugfix: Single probe 3B gets synchronized

Release Notes 1.4.10 - 2020-02-10

  • bugfix: Include sessions data files in pip package

Release Notes 1.4.9 - 2020-02-09

  • Big brainbox merge and release
  • bugfix: clusters.metrics spiking rates accurate
  • probability left for ephys choice world contain generative probabilities, not outcomes

Release Notes 1.4.8 - 2020-01-27

  • ONE Light Windows fixes
  • Installation documentation separates conda and virtualenv options
  • Conda yaml environement file for ibllib

Release Notes 1.4.7

  • ONE Light for behaviour paper data release
  • ONE() standard syntax matching the one light examples

Release Notes 1.4.6

  • Alyx registration: add md5, version and filesize to the pipeline registration
  • Data Patcher: allows to register data from anywhere through FTP/SSH/GLobus
  • ONE Light for behaviour paper data release

Release Notes 1.4.5 Hotfix

  • Ephys extraction: left probability bug when sequence was 0 - fixed

Release Notes 1.4.4

  • Ephys extraction:
    • left probability extracted properly
    • add robustness to audio fronts extraction in FPGA
  • Passive stimulus: raw data registered in pipeline
  • Training extraction: microphone extraction for habituation sessions
  • ALF: specific to_dataframe method for Bunch

Release Notes 1.4.3 Hotfix

  • Ephys extraction: handle fringe case where recording is interrupted in the middle
  • Wheel extraction: if rotary encoder version is outdated and stores data in the wrong unit, auto-detect and output in seconds even for new versions

Release Notes 1.4.2

  • FPGA/bpod events synchronization performed even when their counts do not match
  • Updated requirement versions for mtscomp and phylib

Release Notes 1.4.1

  • wheel extraction outputs a timestamps attribute, not times
  • make the wheel extraction more robust

Release Notes 1.4.0

  • Ephys extraction:
    • un-synchronized spike sortings not uploaded on flat-iron
    • reaction times extracted
    • valve-open times bugfix
  • Wheel extraction:
    • training wheel position and timing are now correct
    • ephys & training: units: radians mathematical convention
  • ONE:
    • Alyx client handles pagination seamlessly

Release Notes 1.3.10 Hotfix

  • cross-platform get of session folder for rig computer copy to server

Release Notes 1.3.9

  • spikeglx.verify_hash() method to check file integrity after transfers/manipulations
  • create wirings settings files on ephys computer transfer to server

Release Notes 1.3.8

  • Ephys Extraction:
    • duplicate probe.trajectories bugfix
    • extraction works with unoperational fram2ttl at beginning of ephys session
    • clusters.metrics.csv has consistent size with npy cluster objects
    • ephys transfer: create ephys extraction flags after the transfer is complete

Release Notes 1.3.7 hotfixes- 21-NOV-2019

  • Rename spike.times on failed sync to reflect the clock as per ALF convention
  • sync 3A fails if first cam event whithin 200ms of start
  • compress ephys goes through a tempfile to not interfere with transfers/globbing

Release Notes 1.3.6 - 20-NOV-2019

  • Ephys Extraction (phylib)
    • convert ks2 amplitudes to volts for spikes.amps, clusters.amps. templates.waveforms, clusters.waveforms to get uV
    • generates Cluster UUIDs file
    • individual spike depths computed from PC features
  • Ephys Synchronization
    • use frame2TTL split for 3A by default, if not found look for right_camera
    • output individual probe sync in ALF timestamps format

Release Notes 1.3.5 - 18-NOV-2019

  • registration ignores ks2alf probes subfolders
  • fix typo in raw qc dataset types

Release Notes 1.3.4 - 18-NOV-2019

  • Alyx registration adds the relative path to session root as dataset.subcollection
  • Ephys extraction:
    • split probe folders output alf/probe00 and alf/probe01 instead of merge
    • outputs templates.waveforms and clusters.waveforms in sparse arrays
    • outputs probes.description and probes.trajectory
    • renamed the raw ephys QC output
    • outputs clusters.metrics
  • Bugfixes:
    • 3B raw ephys QC output ap.file not found on nidq object
    • 3A sync probe threshold set to 2.1 samples

Release Notes 1.3.1 - 12-NOV-2019

  • transfer scripts from ephys/video/rig computers to local servers
  • bugfix spigeglx.glob_ephys_files when metadata file without ap.bin file

Release Notes 1.3.0 - 11-NOV-2019

  • Transfer rig data takes into account session type (ephys/training) to create flags
  • Ephys video compression in pipeline
  • Ephys audio compression in pipeline

Release Notes 1.2.9

  • Ephys extraction: provide full 3B default wirings if files do not exist.

Release Notes 1.2.8

  • Ephys extraction: merge sync ephys in the pipeline overwrites ks2_alf directory if it already exists

Release Notes 1.2.7

  • Added biasedScanningChoiceWorld task to biased extractor for Zador lab

Release Notes 1.2.6

feature/ephys_compression

  • spikeglx.Reader supports mtscomp ephys binaries
  • server pipeline for compression of ephys files

feature/peths

  • brainbox.singlecell.peths with tests
  • brainbox.processing.bincount2D supports aggregation on fixed scale
  • simple examples script and notebook

Release Notes 1.2.5

  • examples/brainbox/plot_peths.py: by Matt. W.
  • examples/brainbox/rasters by Michaël S.
  • Allen Atlas framework and probe registration base functions
  • server pipeline for audio extraction of training sessions