Changelog for Pulse3D

0.34.2 (2023-09-06)

Added:

  • Ability to specify the type of data being analyzed (i.e. Twitch Force, Calcium/Voltage Fluorescence, etc.)

0.34.1 (2023-08-23)

Fixed:

  • Issue with stim data not getting trimmed correctly

0.34.0 (2023-08-22)

Added:

  • Metadata value for H5 files that specifies how many µs to trim from the start of the magnetometer data after running it through the magnet finding algorithm

0.33.14 (2023-08-21)

Fixed:

  • Incorrect metrics for Contraction 10 and Relaxation 90 points

0.33.13 (2023-07-17)

Fixed:

  • Support for MA mini barcodes

  • Issue with certain waveforms causing errors during peak detection

0.33.12 (2023-07-14)

Added:

  • Max Frequency of Peaks to default peak finding params to show in metadata if user-defined

0.33.11 (2023-07-07)

Added:

  • Support for MA mini barcodes

0.33.10 (2023-07-07)

Fixed:

  • Removed unnecessary dependency

0.33.9 (2023-06-29)

Added:

  • Include user-defined peak finding parameters in metadata sheet

  • Ability to add output directory to write_xlsx

  • Performance boost for recordings with high frequency stimulation

  • Ability to use any number of wells in analysis

Changed:

  • Stim Barcode, if found in a recording file, will no longer be included in metadata unless stim data is also found

0.33.8 (2023-06-15)

Added:

  • Support for stimulation subprotocol loops

0.33.7 (2023-06-05)

Fixed:

  • Issue loading from DF when there are more stim timepoints than magnetometer timepoints

  • Issue loading zipped xlsx files

0.33.6 (2023-05-18)

Fixed:

  • Correct use of baselines in Twitch Velocity

0.33.5 (2023-05-17)

Added:

  • Support for python 3.11

0.33.4 (2023-05-08)

Changed:

  • Raise exception when mag finding is unable to converge due to bad data

0.33.3 (2023-05-08)

Added:

  • Time window option to noise-based peak finding

0.33.2 (2023-05-04)

Added:

  • Noise-based peak finding

0.33.1 (2023-05-04)

Added:

  • Changes from 0.32.7

0.33.0 (2023-05-01)

Fixed:

  • Correct use of baseline widths in Twitch AUC, Twitch Amplitude, and Twitch Velocities

0.32.7 (2023-05-02)

NOTE: The date on this release is correct, it was released after 0.33.0, so 0.33.0 does not include these changes

Fixed:

  • Issue with to_dataframe outputting an empty DF when include_stim_data=True and no stim data present

0.32.6 (2023-04-28)

Added:

  • Ability to PlateRecording to handle zip file containing multiple optical xlsx files

0.32.5 (2023-04-27)

Fixed:

  • Correctly calculate upper x bound for snapshot graphs in create_waveform_charts

0.32.4 (2023-04-21)

Changed:

  • Re-add ability to override default magnet finding alg positions

0.32.3 (2023-04-04)

Added:

  • Ability to ignore stim data in to_dataframe

0.32.2 (2023-03-23)

Fixed:

  • Skip reading metadata from missing wells when loading optical files

0.32.1 (2023-03-21)

Fixed:

  • PlateRecording.to_dataframe when loaded from an xlsx input file

0.32.0 (2023-03-16)

Added:

  • Accuracy improvements to the magnet finding algorithm

Changed:

  • Removed ability to override default magnet finding alg positions. This a temporary change will be readded in a future release

0.31.0 (2023-03-16)

Fixed:

  • Update magnet finding algorithm submodule to latest

0.30.6 (2023-03-14)

Fixed:

  • Removed noise filtering and other transforms on optical xlsx input files

0.30.5 (2023-03-13)

Changed:

  • Stim subprotocols no longer continue being draw if they run longer than expected

  • include_stim_protocols is now overrided to True if stim_waveform_format is given

0.30.4 (2023-03-01)

Added:

  • Accuracy improvements to the magnet finding algorithm

Changed:

  • Filtering of data is now applied prior to the magnet finding algorithm instead of after

0.30.3 (2023-02-27)

Added:

  • well_groups param added to PlateRecording to override the well groups in the H5 files

  • Added Platemap Group Metrics to the aggregate-metrics sheet after individual well metrics

Changed:

  • Removed PlateRecording.write_time_force_csv

0.30.2 (2023-02-22)

Changed:

  • peak_detector will now remove timepoints from outside the window provided by start_time and end_time before running the data through the peak finding algorithm. This is too ensure that problematic data outside the window does not interfere with peak finding.

0.30.1 (2023-02-07)

Fixed:

  • Issue with double underscores in file names causing WellFiles to get initialized with the incorrect has_inverted_post_magnet value.

0.30.0 (2023-01-27)

Added:

  • Initial support for PlateMaps, including a new section in the metadata sheet and the PlateMap Labels for each well on the aggregate metrics sheets

0.29.2 (2023-01-24)

Fixed:

  • Calculation of twitch amplitude now correctly interpolates the baseline linearly between the Contraction 10% and Relaxation 90% points.

0.29.1 (2023-01-23)

Fixed:

  • Calculation of twitch amplitude now uses Contraction 10% and Relaxation 90% points for baseline

0.29.0 (2022-12-22)

Added:

  • Graphing of stimulator output waveforms:

    • “Overlayed” display option which graphs stim waveforms in the same chart as the tissue waveforms

    • “Stacked” display which graphs stim waveforms in a separate chart beneath the tissue waveforms chart

  • Ability to interpolate stimulator output waveforms from start timepoints of each subprotocol

0.28.3 (2022-12-08)

  • Fix to_dataframe to include minimum timepoint

0.28.2 (2022-12-08)

  • Show aggregate metrics as long as 1 twitch is present

0.28.1 (2022-12-06)

  • Added option to add stim protocols sheet in analysis output

0.28.0 (2022-11-16)

  • Accuracy and performance improvements to the magnet finding algorithm

  • PlateRecording’s start_time and end_time parameters now take effect before running the magnet finding algorithm. These params are currently only intended to be used for recording snapshots. They have no effect on Beta 1 data

  • Removed use_mean_of_baseline from PlateRecording since the alternative is never used

0.27.5 (2022-11-10)

  • Added Stim Lid Barcode to output file

0.27.4 (2022-11-08)

  • Add ability to flip waveform data of individual wells for Beta 1 data files

0.27.3 (2022-11-01)

  • Fix Post Stiffness factor being incorrectly reported in metadata sheet if an override value is provided

0.27.2 (2022-10-31)

  • Added Post Stiffness factor to metadata sheet of output

  • Changed energy label from Energy (μJ) to Area Under Curve (μN * second)

0.27.1 (2022-10-20)

  • Fixed issue with twitch_width_percents not being sorted

0.27.0 (2022-10-07)

  • Change magnet finding algorithm to account for 180 degree rotation of plates on V1 instrument

  • Fix issue with trying to grab barcode from calibration files

0.26.1 (2022-10-05)

  • Added ability to pass kwargs to use in PlateRecording initialization through PlateRecording.from_directory

0.26.0 (2022-10-04)

  • Added stiffness factor loading from barcode, and option to override the stiffness factor of the barcode

  • Added Time From Peak to Relaxation 10 (seconds) to default output

0.25.4 (2022-09-20) - Added new normalize_y_axis param to disable or enable y axis normalization

0.25.3 (2022-09-15)

  • Added support for multiple optical files in a zip folder

0.25.2 (2022-09-14)

  • Add static method from_dataframe to PlateRecording

  • Add _load_dataframe method to PlateRecording

  • Add get_windowed_peaks_valleys to peak_detection

  • Changed continuous-waveforms excel sheet to begin at start of window of analysis if given, else 0

0.25.1 (2022-08-25)

  • Add twitch_widths to TwitchVelocity and TwitchAUC

0.25.0 (2022-08-23)

  • Added the option to set custom y-axis for output graphs

0.24.9 (2022-08-23)

  • Added to_dataframe method to PlateRecording

0.24.8 (2022-08-15)

  • Added write_xlsx handling of single number input for width and prominence factors

0.24.7 (2022-08-10)

  • Added end_time and start_time params for PlateRecording class

  • Added width and prominence factor to Pulse3D documentation

0.24.6 (2022-08-01)

  • Added width and prominence factors to API. Can now be called from the binder inside the write_excel function

0.24.5 (2022-07-14)

  • Added updated image for the twitch metrics diagram used in the documentation

  • Added ability for user to add any twitch width instead of only multiples of 5

  • Fixed delayed recording bug

0.24.4 (2022-07-12)

  • Added baseline_widths_to_use to write_xlsx args to replace existing baseline metric

  • Default baseline metric changed to C10 and R90

0.24.1 (2022-06-21)

  • Rename constant for UUID value

  • Add Apple M1 chip support

0.24.0 (2022-06-17)

  • Add support for V1 Mantarray data files

0.23.9 (2022-06-08)

  • Change write_xlsx to return name of generated output file

0.23.8 (2022-05-12)

  • Updated column and index values to well names and seconds for write_time_force_csv method

0.23.7 (2022-05-11)

  • Add write_time_force_csv method to PlateRecording

  • Updated diagram png

0.23.6 (2022-04-14)

  • Fixed issue where desired twitch widths weren’t being output in aggregate metrics sheet

  • Fixed code snippets in documentation

  • Changed output file name to include input file name

  • Removed name param of write_xlsx function

0.23.5 (2022-04-07)

  • Added metadata for stim barcode

0.23.4 (2022-03-10)

  • Fix optical recording file loading

  • Change indexing into excel spreadsheet rows

0.23.3 (2022-02-11)

  • Fix Beta 2 files analysis speed up

0.23.2 (2022-02-11)

  • Optimize metrics functions, lexsort issues, and dataframe pre-processing

0.23.1 (2022-02-11)

  • Fix Beta 2 files analysis speed up

0.23.0 (2022-02-10)

  • 10x speed up for analysis of Beta 2 files

0.22.4 (2022-02-09)

  • Add Beta 2 metadata UUIDs

0.22.3 (2022-02-09)

  • sort_index, not sort_value

0.22.2 (2022-02-09)

  • sort_index

0.22.1 (2022-02-09)

  • Convert time_points to pd.Series

0.22.0 (2022-02-07)

  • Incorporate windowed waveform-analysis

0.21.1 (2022-01-12)

  • Parameterized peak_detection.peak_detector for minimum prominence and width scaling

  • Changed default scaling factors to make peak-finding more sensitive

0.20.2 (2022-01-12)

  • Fixed install issues

0.20.1 (2022-01-11)

  • Improved magnet finding algorithm performance

0.20.0 (2022-01-07)

  • Added Beta 2.2 support

  • Fixed conversion of Beta 2.2 position data to force

0.19.0 (2021-12-08)

  • refactor, rename

0.18.1 (2021-10-20)

  • Fixed offset peak detection

0.17.1 (2021-09-24)

  • SkM metrics

0.16.1 (2021-07-21)

  • Multi zip

0.15.0 (2021-04-27)

  • Added Twitch Interval Irregularity metric to the per twitch metrics page and the aggregate metrics page

0.14.0 (2021-04-20)

  • Added Twitch Width metrics to the per twitch metrics sheet and aggregate metrics sheet

  • Added Twitch Contraction adn Relaxation Coordinates to the per twitch metrics sheet

  • Fixed twitch directionality to default to point upwards for force data

0.13.3 (2021-04-05)

  • Ignore hidden files when listing platereading files

0.13.2 (2021-03-29)

  • Bumped version to refresh MyBinder cache

0.13.1 (2021-03-23)

  • Bumped version to refresh MyBinder cache

0.13.0 (2021-03-19)

  • Added ability to analyze multiple recordings at once by traversing subdirectories

0.12.0 (2021-03-18)

  • Incorporated v0.7.0 of waveform-analysis, changing the units of metrics to force

0.11.0 (2021-03-03)

  • Added Twitch Relaxation Velocity and Contraction Velocity metrics to per twitch metrics sheet and aggregate metrics sheet

0.10.3 (2021-02-24)

  • Testing new publish workflow

0.10.2 (2021-02-17)

  • Incorporated v0.5.11 of waveform-analysis, patching some issues with peak detection

0.10.1 (2021-01-19)

  • Bumped Docker Container to 3.9.1-slim-buster

  • Added message in Jupyter Notebook if not running the latest version

0.10.0 (2021-01-15)

  • Added twitch frequencies chart excel sheet.

  • Added force frequency relationship chart excel sheet.

0.9.0 (2021-01-06)

  • Added Area Under the Curve metric to per twitch metrics sheet and aggregate metrics sheet

  • Fixed issue with interpolation values outside of the given boundaries for optical data.

0.8.2 (2020-12-29)

  • Fixed issue with getting the incorrect well index from the well name for optical data.

0.8.1 (2020-12-20)

  • Added Python 3.9 support.

  • Added steps to documentation explaining how to analyze multiple zip files.

  • Changed formatting of .xlsx output file names to match input the formatting of the input file names. A discrepancy still exists between the input and output file names, however.

  • Added excel sheet for per twitch metrics.

0.8.0 (2020-11-11)

  • Added excel sheet for full length charts.

  • Fixed issue with pure noise files causing errors.

0.7.3 (2020-11-05)

  • Fixed issue with twitches point up field for optical data.

  • Fixed case sensitivity issue (‘y’ and ‘Y’ both work now).

  • Fixed issue causing change of chart bounds to be tedious.

  • Fixed Y axis label for optical data (now ‘Post Displacement (microns)’).

  • Fixed many of the issues causing two consecutive relaxations to be detected incorrectly.

  • Fixed interpolation bugs.

  • Fixed documentation issues.

  • Changed Sampling / Frame Rate from period in seconds to a rate in Hz.

0.7.1 (2020-10-20)

  • Fixed issue with markers in optical data charts.

0.7.0 (2020-10-15)

  • Added ability to analyze optical data entered in an excel template.

  • Added firmware version to excel metadata sheet.

0.6.0 (2020-10-07)

  • Added numbered steps to getting started documentation.

  • Added contiuous-waveform-plots sheet to excel file generation. Currently, the only format for chart creation is a <= 10 second “snapshot” of the middle data points. It shows waveforms as well as Contraction and Relaxation markers on twitches.

  • Added access to reference sensor data.

  • Added performance improvements for accessing raw data.

  • Added ability to upload zip files to Jupyter and updated Getting Started documentation to show how to do so.

  • Changed all interpolation to 100 Hz.

  • Changed default filter for 1600 µs sampling period from Bessel Lowpass 30Hz to Butterworth Lowpass 30Hz.

  • Fixed peak detection algorithm so it is less likely to report two contractions/relaxations of a twitch in a row.

0.5.0 (2020-09-21)

  • Added logging to write_xlsx.

  • Added backwards compatibility with H5 file versions >= 0.1.1.

0.4.1 (2020-09-16)

  • Added Jupyter getting started documentation.

0.4.0 (2020-09-16)

  • Added support for MyBinder.

  • Added Peak Detection Error handling.

  • Added function to create stacked plot.

0.3.0 (2020-09-09)

  • Added generation of Excel file with continuous waveform and aggregate metrics.

  • Added SDK version number to metadata sheet in Excel file.