Changelog - dattalab/moseq2-app GitHub Wiki

v1.1.2 03-02-2022

  • Bug fixes for Arena mask detection tool

v1.1.1 02-16-2022 PUBLIC RELEASE

  • Bug fixes
  • Updated Wiki and notebook documentations

v1.1.1beta 02-12-2022

  • Bug fixes
  • Updated Wiki and notebook documentations
  • Removed speed and scalar threshold from transition graphs
  • Changed graph layouts
  • Removed linear classifier in the analysis and modeling notebook

v1.1.0beta 02-16-2022

  • Bug fixes
  • Updated Wiki and notebook documentations
  • All figures now exportable
  • Changed Interactive ROI Detection Tool to Interactive Arena Detection Tool
  • Updated dask and related packages in moseq2-pca

v1.1.0beta 02-16-2022

  • Bug fixes
  • Updated Wiki and notebook documentations
  • All figures now exportable
  • Changed Interactive ROI Detection Tool to Interactive Arena Detection Tool
  • Fix kernel death issues in in moseq2-pca

1.0.2beta / 11-18-2021

  • Update to moseq2-app == 1.0.2beta
  • Update to moseq2-model == 1.0.1beta
  • Update to moseq2-viz == 1.0.2beta

1.0.1beta / 11-08-2021

  • Update to moseq2-extract == 1.0.1beta
  • Update to moseq2-pca == 1.0.1beta
  • Update to moseq2-viz == 1.0.1beta

1.0.0beta / 08-20-2021

  • Update to moseq2-extract == 1.0.0beta
  • Update to moseq2-pca == 1.0.0beta
  • Update to moseq2-model == 1.0.0beta
  • Update to moseq2-viz == 1.0.0beta

0.2.0 / 06-01-2020

  • Update to moseq2-extract == 0.5.0

  • Update to moseq2-pca == 0.3.0

  • Update to moseq2-model == 0.4.0

  • Update to moseq2-viz == 0.3.0

    Cross-Repo Common Edits

  • Added complete codebase documentation.

  • Added unit testing+integration testing suites.

  • Added Makefile to download test data from S3 bucket, (used for TravisCI testing)

  • Updated travisCI testing protocol; created job matrices testing MoSeq2 on python versions >=3.6

  • Refactored codebase to use wrapper functions, merging functionality between CLI and GUI

  • Locked all setup.py dependency versions

  • Added installed-version checking cli command

0.1.3 / 06-02-2019

0.1.2 / 01-14-2019

0.1.1 / 10-04-2018

0.1.0 / 2018-08-20

  • First release!

Latest / 2020-06-01

Cross-Repo Common Edits

  • Added complete codebase documentation.
  • Added unit testing+integration testing suites.
  • Added Makefile to download test data from S3 bucket, (used for TravisCI testing)
  • Updated travisCI testing protocol; created job matrices testing MoSeq2 on python versions >=3.6
  • Refactored codebase to use wrapper functions, merging functionality between CLI and GUI
  • Locked all setup.py dependency versions
  • Added installed-version checking cli command

moseq2-extract == 0.5.0

  • Total coverage=81%.
  • Added Jupyter Notebook compatible functionality
    • Added troubleshooting capabilities: sample extractions, rois + previews
    • Added option to extract/re-extract select recordings
  • Added index file generation utility (moved from moseq2-viz)
  • Added aggregate_results functionality
  • Added safer extract-overwriting policy
  • Added support for Azure cameras
  • Added support for concave-shaped arenas (\_/)

moseq2-pca == 0.3.0

  • Total coverage=83%.
  • Added Jupyter Notebook compatible functionality
  • Added safer PCA training-overwriting policy
  • Re-added user-defined h5-path option, per Issue #55
  • Bug fixes

moseq2-model == 0.4.0

  • Total coverage=86%.
  • Added Jupyter Notebook compatible functionality
    • Added option to model select groups/sessions
  • Updated model-training checkpoint functionality
  • Added default validation partitioning via scikit-learn train_test_split
  • Added verbose model training capability, allows for plotting log-likelihoods across training iterations.

moseq2-viz == 0.3.0

  • Total coverage=81%.
  • Added Jupyter Notebook compatible functionality
  • Added capability to use custom colors for almost all plotting functions.
  • Updated usage plotting functionality
    • Added safer group selection method for plotting
    • Added capability to sort syllables by mutant-ness with respect to any given plotting statistic (usage, syllable duration, syllable speed).
  • Added position heat-map graphing functionality (by group or by individual session)
  • Added syllable speed compute and graphing capabilities (based on rodent's centroid speed)

0.1.3 / 2019-06-02

moseq2-extract

  • Cleanup of h5 file structure
  • h5 files now include more useful metadata
  • Added support for sorting ROIs
  • Added the copy-slice utility
  • Added support for extraction directly from tarballs
  • Fixed statsmodel incompatibility with new scipy

moseq2-pca

  • Upgraded joblib
  • Simplified installation
  • Fixed timestamp bug #43

moseq2-model

  • Upgraded joblib
  • Updated regularization and normalization options
  • Clean up setup.py

moseq2-viz

  • Fixed jitter issue with crowd movies
  • Fixed flickering in crowd movies
  • Numerous feature improvements

moseq2-batch

  • Numerous feature improvements

0.1.2 / 2019-01-14

moseq2-extract

  • Added hole-filling to ROI detection
  • Switched to new OpenCV 4 API (note that you must re-run pip install so that the correct version of OpenCV is used)

moseq2-pca

  • Addressed #45

moseq2-model

  • Added support for parallel processing

moseq2-viz

  • Added new distance metrics
  • Addressed #40
  • Addressed #36
  • Addressed #32

0.1.1 / 2018-10-04

moseq2-extract

  • Fixed packaging
  • Added ffv1 conversion for data compression
  • Made tracking more robust per issue #42
  • Made initialization of tracking model more robust
  • Added gradient filtering for ROI detection in noisy environments

moseq2-pca

  • Fixed packaging
  • Fix for slurm initialization
  • Added bash completion scripts
  • Addressed #38
  • Now prints more useful information on Dask initialization

moseq2-model

  • By default kappa is set to the number of frames
  • Added bash completion

moseq2-viz

  • Added ability to center and rotate mouse for crowd movies
  • Fixed issue with feedback paths
  • Fixed packaging
  • Added information metrics per #28
  • Added graphviz layout algorithms
  • Added lots of options for laying out transition graphs
  • Addressed #33

moseq2-batch

  • Fixed packaging
  • Added ffv1 conversion support
  • Pinned joblib version
  • Updated ruamel.yaml
  • Cleaned up yaml status reports for batch jobs
  • Addressed issue #9

0.1.0 / 2018-08-20

First release!

moseq2-extract

  • More explicit metadata for extracted data

moseq2-pca

  • Cleaned up handling of Dask computations for PCA

moseq2-viz

  • Lots of features added to moseq2-viz
  • Added ability to visualize differences between graphs
  • Added scalar visualization
  • Added better handling of add-group
  • Updated format of moseq2-index.yaml note that this is a breaking change, users of older versions will need to regenerate the index file
  • Commented important functions to use in notebooks