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 wheninclude_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 toTrue
ifstim_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 toPlateRecording
to override the well groups in the H5 filesAdded
Platemap Group Metrics
to theaggregate-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 bystart_time
andend_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
’sstart_time
andend_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 dataRemoved
use_mean_of_baseline
fromPlateRecording
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)
toArea 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 throughPlateRecording.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 PlateRecordingAdd
_load_dataframe
method to PlateRecordingAdd
get_windowed_peaks_valleys
to peak_detectionChanged
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
andTwitchAUC
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
towrite_xlsx
args to replace existing baseline metricDefault 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 ofwrite_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 scalingChanged 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.