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release_notes.md

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Changelog

[1.6.2] - 2025-01-06

added

  • scipy.signal.ricker has been removed and is now available at ibldsp.utils.ricker

[1.6.1] - 2025-01-03

fixed

  • waveforms extractor returns a list of files for registration

changed

  • moved the repo contribution guide to automatic ruff formatting

[1.6.0] - 2024-12-06

added

  • single derivative option for CSD for RIGOR metrics
  • radon forward and inverse transforms
  • support headerless binary files (open ephys)

fixed

  • cadzow iterations
  • numpy 2.0 support
  • destripe with channels=False

[1.5.0] - 2024-10-24

  • Automatic sorting per shank / row / col
  • Minimum Python version is 3.10

[1.4.0] - 2024-10-05

  • Waveform extraction:
    • Optimization of the waveform extractor, outputs flattened waveforms
    • Refactoring ot the waveform loader with back compability
  • Bad channel detector:
    • The bad channel detector has a plot option to visualize the bad channels and thresholds
    • The default low-cut filters are set to 300Hz for AP band and 2 Hz for LF band

1.3.2 2024-09-18

  • Hotfix for WaveformsLoader label ids

1.3.1 2024-09-05

  • Hotfix for running tests with PyPI install

1.3.0 2024-09-05

  • Add support for NPultra high-density probes
  • NumPy and SciPy version floors

1.2.1 2024-08-20

  • bugfix waveform extraction: fix logic when channel labels is not None

1.2.0 2024-08-01

  • Adds ibldsp.waveform_extraction.WaveformsLoader, an interface for waveforms extracted by extract_wfs_cbin.

1.1.3 2024-07-11

  • Add features and tests for extract_wfs_cbin, including various preprocessing options.

1.1.2 2024-07-03

  • bugfix waveform extraction: reverting refactoring of the function to maintain compatibility with current ibllib

1.1.1 2024-06-07

  • Add support for NP2.0 prototype probe with probetype 1030

1.0.1 2024-05-29: support for waveform extraction on non-standard electrode layouts

  • bugfix waveform extraction: the probe channel layout is inferred from the spikeglx metadata by default
  • bugfix waveform extraction: the channel neighnourhood fill value is the last channel index + 1 by default instead of 384

1.0.0 2024-04-22

  • Functionalities to check and mitigate saturation in neuropixel recordings
    • spikeglx.Reader has a range_volts method to get the saturating voltage value for a given type of probe
    • ibldsp.voltage.saturation() is a function that returns a boolean array indicating which samples are saturated, and a mute function
    • ibldsp.voltage.decompress_destripe_cbin saves a _iblqc_ephysSaturation.samples.npy and applies the mute function post-destriping

0.10.3 2024-04-18

  • Patch fixing memory leaks for waveform_extraction module.

0.10.2 2024-04-10

  • Add waveform_extraction module to ibldsp. This includes the extract_wfs_array and extract_wfs_cbin methods.
  • Add code for performing subsample shifts of waveforms.

0.10.1 2024-03-19

  • ensure compatibility with spikeglx 202309 metadata coordinates

0.10.0 2024-03-14

  • add support for online spikeglx reader

0.9.2 2024-02-08

  • neurodsp is now ibldsp. Drop-in replacement of the package name is all that is required to update. The neurodsp name will disappear on 01-Sep-2024; until then both names will work.

0.9.0 2024-01-17

  • neurodsp.utils.sync_timestamps: uses FFT based correlation to speed up large arrays alignments
  • waveforms: new wiggle plot for multi-trace waveforms

0.8.1 2023-09-21

  • revert to reading channel info from private methods in shank splitting NP2.4 code to get the original channel layout from shank metadata file

0.8.0 2023-09-01

  • add compatibility with spikeglx metadata version 2023-04 to get probe geometry

0.7.0 2023-06-29

  • Add function spike_venn3 in new module neurodsp.spiketrains
  • Update iblutil dependency to 1.7.0 to use iblutil.numerical.bincount2D

0.6.2 2023-06-19

  • add option to specify meta-data file for spikeglx.Reader

0.6.1 2023-06-06

  • Fix bug in ADC cycles sampling for Neuropixel 1.0 probes

0.6.0 2023-05-15

  • Add waveforms utilities for spike features computations

0.5.3 2023-04-24

  • Fix for cases where channel map keys are not present

0.5.2 2023-04-19

  • Geometry now supports both snsShankMap and snsGeomMap fields
  • Option to compute LFP without splitting shanks

0.5.1 2023-03-07

  • Enforce iblutil dependency

0.5.0 2023-03-06

  • KCSD option for LFP current source density
  • Cadzow for NP1: expose spatial parameters for LFP

0.4.1 2022-11-29

  • CAT GT command in meta file

0.4.0 2022-10-28

  • current source density simple double diff with denoising from raw LFP

0.3.2 2022-10-27

  • spikeglx geometry chops the ADC sample shift to the number of channels to accomodate legacy 3A probes with 276 channels
  • agc: gain refers to the inverse of applied gains for agc - done to handle dead channels in destriping

0.3.1

  • neurodsp.utils.rises / falls: detects rising and falling edges of oversampled analog signals
  • neuropixel: add functions to reconstruct original files from split NP2.4 files

minor changes

  • support for returning number of shanks from metadata

0.2.2

  • BUGFIX change getattr of neuropixel to allow for stared imports

0.2.1

  • BUGFIX constant SYNC_PIN_OUT re-introduced in ibl-neuropixel

0.2.0

  • destripe_decompress_cbin: add a parameter to output QC in a different location to accomodate pykilosort scratch dir
  • support for NP2.4 and NP2.1 geometries on spikeGlx

minor changes

  • deprecated SITES_COORDINATES that would default on Neuropixel 1.0 early generations (3A probes with 374 channels)
  • spikeglx compress: pass dtype to mtscomp