https://github.com/alleninstitute/openscope_databook - March Madness

• add notebooks for openscopes 2025 data release; sequence learning, temporal barcoding, and vision 2 hippocampus
• update install and environment
• update links
• bug fixes
• typo fixes

- Python
Published by rcpeene about 1 year ago

https://github.com/alleninstitute/openscope_databook - Dressings for DOI

• Add many new contributors' information to contributors.csv
• Add visualize2pvr_behavior notebook
• Remove warning output in all notebooks
• Add download bar for download notebook
• Update environment
• Improve markdown in several notebooks
• Minor plot improvements
• Fix typos

- Python
Published by rcpeene almost 2 years ago

https://github.com/alleninstitute/openscope_databook - Publishing Potluck

• Added GLM notebook
• Added behavioral state notebook from @sjara
• Improved illusion notebook with changes from @yrk24
• Implemented changes in basics and visualizations chapter as per @stephprince's review
• Improved authors list and authors index formatting and generation
• Change file streaming notebook to use remfile instead of fsspec
• Remove extraneous warnings from all notebooks
• Updated dependencies
• Added codespell
• Typo and small fixes in many notebooks

- Python
Published by rcpeene about 2 years ago

https://github.com/alleninstitute/openscope_databook - OpenScope Databook

• Added three notebooks introducing OpenScopes three newly released datasets
• Small changes

- Python
Published by rcpeene over 2 years ago

https://github.com/alleninstitute/openscope_databook - Riddles and Refinement

• Improved the "Tensor Decomposition of Spiking Activity Through Trials" notebook
• Altered dependency versions
• Skip long steps in a few notebooks during testing
• Turned automatic author/version insertion into a Sphinx Extension

- Python
Published by rcpeene over 2 years ago

https://github.com/alleninstitute/openscope_databook - Machine Learning and Human Learning

• Added Higher-order chapter
• Add Stim Templates Visualization notebook
• Added Suite2P Segmentation notebook
• Added CEBRA notebook
• Added TCA notebook
• Added Waveforms Visualization notebook
• Improved Optotagging notebook with new dandiset, analysis bugfixes
• Optimization to metadata notebook
• Added Google Analytics
• Bumped Jupyter book version
• Updated logo to new OpenScope logo
• Improved instructions in front page
• Improved methods section
• Changed way NWBs are printed
• Added citations for technologies referenced
• Fixed typos and formatting

- Python
Published by rcpeene over 2 years ago

https://github.com/alleninstitute/openscope_databook - Analysis, Environments, Infrastructure, Organization, Utilities, and sometimes Y

• Added dynamic insertion of authors list from contributors
• Added bibliography and citations to notebooks
• Made databook_utils package to contain some utilities for the repo and code reused in many notebooks
• Simplified Requirements to just direct dependencies
• Made Environment setup cell in notebooks work for all environments
• Added 2P Inclusion Criteria notebook
• Added FAQ
• Changed logo to Neuraldynamics
• Added Credit Assignment Reproducing Figures notebook
• Added methods chapter to notebook
• Added 2P Modality Alignment notebook
• Added folder of notebooks using embargoed dandisets
• Added spike matrix notebook
• Added version number to top of intro page
• Small changes to notebooks and markdown

- Python
Published by rcpeene almost 3 years ago

https://github.com/alleninstitute/openscope_databook - Google Colab integration and more first-order analysis.

Added integration with Google Colab, and added two new notebooks; Current Source Density analysis and ROI Cell Matching between days.

- Python
Published by rcpeene about 3 years ago

https://github.com/alleninstitute/openscope_databook - NWB Reference Schemas, Running Plots, Unit Drift Plots

Added tables which can be used as a reference to explain all the fields in OpenScope's NWB files. Also added running plots to and renamed visualizeeyetracking to visualizebehavior. Finally, added plots which explain Unit drift to visualizeunit_metrics.

- Python
Published by rcpeene over 3 years ago

https://github.com/alleninstitute/openscope_databook - Additional QC Plots and Dandiset Metadata Notebook

Creation of a new notebook that generates a table of metadata about the sessions in a dandiset. Also added three new plots, inspired by our QC plots, to two existing notebooks.

- Python
Published by rcpeene over 3 years ago

https://github.com/alleninstitute/openscope_databook - Front Page Improvement

Some documentation fixes and improvements to accomodate latest changes. Also added the newest content to the table of contents.

- Python
Published by rcpeene over 3 years ago

https://github.com/alleninstitute/openscope_databook - Neuronal Units and 2P Responses Visualizations

Three new notebooks; Neuronal Unit Metrics Evaluation/Visualization and Neuronal Units Responses to Stimulus Visualization for Ecephys, and 2P DFF Responses to Stimulus Visualization for Ophys.

- Python
Published by rcpeene over 3 years ago

https://github.com/alleninstitute/openscope_databook - 2P Raw and Eye Tracking Visualization

Addition of 2-Photon raw movie visualization, eye tracking visualization, documentation additions, and a number of notebook improvements.

- Python
Published by rcpeene over 3 years ago

https://github.com/alleninstitute/openscope_databook - LFP Responses Visualization

General changes to all notebook structures for usability, and addition of notebook which creates visualizations of LFP responses to stimulus events.

- Python
Published by rcpeene over 3 years ago

https://github.com/alleninstitute/openscope_databook - Primordial Release

Very first release of Databook. It is not yet production-ready and is not yet public.

- Python
Published by rcpeene over 3 years ago