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GitHub / alleninstitute/openscope_databook issues and pull requests

#447 - update/add new get_unit_locations code to databook

Issue - State: open - Opened by rcpeene 4 months ago

#446 - update zenodo release info

Issue - State: open - Opened by rcpeene 4 months ago

#445 - request: apply rastermap

Issue - State: open - Opened by bendichter 5 months ago

#444 - improvement: receptive fields

Issue - State: open - Opened by bendichter 5 months ago

#443 - Cython required beforehand

Issue - State: open - Opened by RobertoDF 5 months ago

#442 - Dev

Pull Request - State: closed - Opened by rcpeene 5 months ago - 1 comment

#441 - Fix minor spelling error

Pull Request - State: closed - Opened by kabilar 5 months ago - 1 comment

#440 - Update Dandihub instructions

Pull Request - State: closed - Opened by kabilar 5 months ago - 1 comment

#439 - Improve Sequence Learning Notebook with Michael Berry's improvements

Issue - State: closed - Opened by rcpeene 5 months ago - 1 comment

#438 - Add sequence learning showcase nb rough draft

Pull Request - State: closed - Opened by rcpeene 7 months ago - 1 comment

#437 - Pr

Pull Request - State: closed - Opened by rcpeene 7 months ago - 1 comment

#436 - Update URL for DANDI Docs

Pull Request - State: closed - Opened by kabilar 7 months ago

#100 - Test notebook on Dandihub, figure out fastest way

Issue - State: closed - Opened by rcpeene over 2 years ago - 1 comment
Labels: enhancement

#99 - Neuropixel probes

Pull Request - State: closed - Opened by rcpeene over 2 years ago - 1 comment

#98 - Adjust README and front page of Databook

Issue - State: closed - Opened by rcpeene over 2 years ago - 2 comments
Labels: enhancement

#97 - Make data access utility to select streaming or download

Issue - State: closed - Opened by rcpeene over 2 years ago - 1 comment
Labels: enhancement

#96 - Organize imports

Issue - State: closed - Opened by rcpeene over 2 years ago
Labels: enhancement

#95 - Change eye tracking notebook to use file streaming

Issue - State: closed - Opened by rcpeene over 2 years ago
Labels: enhancement

#94 - Modify notebooks to use environment variable for dandi api key

Issue - State: closed - Opened by rcpeene over 2 years ago - 3 comments
Labels: enhancement

#93 - Resolve different filepaths with Thebe

Issue - State: closed - Opened by rcpeene over 2 years ago - 2 comments
Labels: enhancement

#92 - Neuropixel probes

Pull Request - State: closed - Opened by rcpeene over 2 years ago - 2 comments

#91 - Color markers in neuropixel probes notebook

Issue - State: closed - Opened by rcpeene over 2 years ago - 1 comment
Labels: enhancement

#90 - Added completed Eye tracking notebook

Pull Request - State: closed - Opened by rcpeene over 2 years ago - 3 comments

#89 - Improved 2p raw notebook usability

Pull Request - State: closed - Opened by rcpeene over 2 years ago - 1 comment

#88 - 2p raw

Pull Request - State: closed - Opened by rcpeene over 2 years ago - 1 comment

#87 - Alter neuropixel display script to use ccfwidgets

Issue - State: closed - Opened by rcpeene over 2 years ago - 14 comments
Labels: enhancement

#86 - Adjust CI workflows to run on more branches

Issue - State: closed - Opened by rcpeene over 2 years ago - 1 comment
Labels: enhancement

#85 - Improvements and Fixes to LFP Response notebook

Pull Request - State: closed - Opened by rcpeene over 2 years ago - 1 comment

#84 - Test notebooks with github actions

Issue - State: closed - Opened by rcpeene over 2 years ago - 4 comments
Labels: enhancement

#83 - Adding 2p raw notebook to next release

Pull Request - State: closed - Opened by rcpeene over 2 years ago - 1 comment

#82 - Optimize LFP notebook so interpolation consumes less memory

Issue - State: closed - Opened by rcpeene over 2 years ago - 6 comments
Labels: bug

#81 - Explore hosting options other than mybinder.org

Issue - State: closed - Opened by rcpeene over 2 years ago - 2 comments
Labels: question

#80 - Move 'filename' definition

Issue - State: closed - Opened by rcpeene over 2 years ago
Labels: enhancement

#79 - Fix filepath functionality on binder

Issue - State: closed - Opened by rcpeene over 2 years ago - 2 comments
Labels: bug

#78 - Interpolate 2p fluorescence to match 2p movie

Issue - State: closed - Opened by rcpeene over 2 years ago - 4 comments
Labels: enhancement

#77 - Fix CI bug in LFP notebook

Issue - State: closed - Opened by rcpeene over 2 years ago - 3 comments
Labels: bug

#76 - Figure out how to clear fsspec cache

Issue - State: closed - Opened by rcpeene over 2 years ago - 2 comments
Labels: enhancement

#75 - Fix hertz unit usage in LFP

Issue - State: closed - Opened by rcpeene over 2 years ago - 1 comment
Labels: bug

#74 - Add axis labels

Issue - State: closed - Opened by rcpeene over 2 years ago - 1 comment
Labels: enhancement

#73 - Develop an eye tracking visualization notebook

Issue - State: closed - Opened by jeromelecoq over 2 years ago - 7 comments
Labels: enhancement

#72 - Deploy denoising notebook onto uploaded NWB files with Raw

Issue - State: closed - Opened by jeromelecoq over 2 years ago - 3 comments
Labels: enhancement

#71 - Include depth in LFP axis

Issue - State: closed - Opened by rcpeene over 2 years ago - 7 comments
Labels: enhancement

#70 - Evaluate ability to use docker with binders and as a base test environment

Issue - State: closed - Opened by jeromelecoq over 2 years ago - 1 comment
Labels: enhancement, question

#69 - Error with fsspec: "No space left on device"

Issue - State: closed - Opened by rcpeene over 2 years ago - 2 comments
Labels: bug

#68 - Update nwbwidget version

Issue - State: closed - Opened by rcpeene over 2 years ago - 5 comments
Labels: enhancement

#67 - Handle cross-platform filepaths within notebook

Issue - State: closed - Opened by rcpeene over 2 years ago - 2 comments
Labels: enhancement

#66 - Allow for variable that sets interpolation units in LFP notebook

Issue - State: closed - Opened by rcpeene over 2 years ago - 2 comments
Labels: enhancement

#65 - Discuss cross-platform compatibility with environment

Issue - State: closed - Opened by rcpeene over 2 years ago - 2 comments
Labels: question

#64 - Commit notebooks with output

Issue - State: closed - Opened by rcpeene over 2 years ago - 1 comment
Labels: enhancement

#63 - Add download cells to the top of notebooks

Issue - State: closed - Opened by rcpeene over 2 years ago - 8 comments
Labels: enhancement

#62 - Ensure consistent formatting in markdown between notebooks

Issue - State: closed - Opened by rcpeene over 2 years ago - 1 comment
Labels: enhancement

#61 - Environment

Pull Request - State: closed - Opened by rcpeene over 2 years ago

#60 - Add mpl_interactions to environment

Issue - State: closed - Opened by rcpeene over 2 years ago - 1 comment

#59 - Release LFP notebook

Pull Request - State: closed - Opened by rcpeene over 2 years ago - 7 comments

#58 - Visualize lfp

Pull Request - State: closed - Opened by rcpeene over 2 years ago

#57 - Fixes for binder and Thebe compatibility.

Pull Request - State: closed - Opened by rcpeene over 2 years ago

#56 - test

Issue - State: closed - Opened by rcpeene over 2 years ago

#55 - Removed pip installs in notebooks

Issue - State: closed - Opened by rcpeene over 2 years ago - 1 comment
Labels: enhancement

#54 - Make 2p raw data access notebook

Issue - State: closed - Opened by rcpeene over 2 years ago - 14 comments
Labels: enhancement

#53 - Change file paths in all scripts to work with thebe and binder

Issue - State: closed - Opened by rcpeene over 2 years ago - 1 comment
Labels: enhancement

#52 - Removed test thebe notebook

Pull Request - State: closed - Opened by rcpeene over 2 years ago

#51 - Figure out best way to manage files with Thebe in Jupyter Book

Issue - State: closed - Opened by rcpeene over 2 years ago - 3 comments
Labels: question

#50 - Include thebe test in book

Pull Request - State: closed - Opened by rcpeene over 2 years ago

#49 - Identify best way to test deployment/thebe/binder changes without interfering with production

Issue - State: closed - Opened by rcpeene over 2 years ago - 2 comments
Labels: enhancement, question

#48 - Added temp notebook to test thebe filesystem

Pull Request - State: closed - Opened by rcpeene over 2 years ago

#47 - Probes show up on one plane with 100 micrometer brain atlas

Issue - State: closed - Opened by rcpeene over 2 years ago - 8 comments
Labels: bug

#46 - Dev

Pull Request - State: closed - Opened by rcpeene over 2 years ago

#45 - Fix streaming code with nwbwidgets

Issue - State: closed - Opened by rcpeene over 2 years ago
Labels: bug

#44 - Modified postBuild to fix command

Pull Request - State: closed - Opened by rcpeene over 2 years ago

#43 - Dev

Pull Request - State: closed - Opened by rcpeene over 2 years ago

#42 - Binder kernel crashes with brainrender script

Issue - State: closed - Opened by rcpeene over 2 years ago - 13 comments
Labels: bug

#41 - Dev

Pull Request - State: closed - Opened by rcpeene over 2 years ago - 1 comment

#40 - Alter Jupyter configuration parameters on Binder

Issue - State: closed - Opened by rcpeene over 2 years ago - 2 comments
Labels: enhancement

#39 - added apt.txt so binder will install os dependencies

Pull Request - State: closed - Opened by rcpeene over 2 years ago

#38 - Removed pywin requirement

Pull Request - State: closed - Opened by rcpeene over 2 years ago

#37 - Recreated environment for Python 3.8

Pull Request - State: closed - Opened by rcpeene over 2 years ago

#36 - Fixed runtime.txt for binder

Pull Request - State: closed - Opened by rcpeene over 2 years ago

#35 - Added runtime.txt in hopes that it will get binder launch working

Pull Request - State: closed - Opened by rcpeene over 2 years ago

#34 - Removed environment.yml, was preventing requirements.txt from being u…

Pull Request - State: closed - Opened by rcpeene over 2 years ago

#33 - Renamed invalid filename in toc

Pull Request - State: closed - Opened by rcpeene almost 3 years ago

#32 - Removed extraneous comments in toc

Pull Request - State: closed - Opened by rcpeene almost 3 years ago

#31 - Dev

Pull Request - State: closed - Opened by rcpeene almost 3 years ago

#30 - Try to file stream with raw data 2p nwb

Issue - State: closed - Opened by rcpeene almost 3 years ago - 2 comments
Labels: enhancement

#29 - Add Github workflow for testing environment

Issue - State: closed - Opened by rcpeene almost 3 years ago - 2 comments
Labels: enhancement

#28 - Dev

Pull Request - State: closed - Opened by rcpeene almost 3 years ago

#27 - Add documentation for setting up environment on local machine

Issue - State: closed - Opened by rcpeene almost 3 years ago - 3 comments
Labels: documentation

#26 - Environment

Pull Request - State: closed - Opened by rcpeene almost 3 years ago

#25 - Added completed 'streaming nwb' notebook

Pull Request - State: closed - Opened by rcpeene almost 3 years ago

#24 - Updates to all notebooks, addition of neuropixel probe visualization notebook

Pull Request - State: closed - Opened by rcpeene almost 3 years ago - 1 comment

#23 - Ensure launch button works in book

Issue - State: closed - Opened by rcpeene almost 3 years ago - 2 comments
Labels: enhancement

#22 - Establish a shared framework for accessing nwb files across notebooks: How do we want to do this?

Issue - State: closed - Opened by jeromelecoq almost 3 years ago - 2 comments
Labels: question

#21 - Make a notebook demonstrating basic usage of pynwb and reading in an NWB file

Issue - State: closed - Opened by rcpeene almost 3 years ago - 1 comment
Labels: enhancement

#20 - Determine a small set of good demo nwb files for use by the databook scripts

Issue - State: closed - Opened by rcpeene almost 3 years ago - 2 comments
Labels: question

#18 - Deleted placeholder visualization files. Added neuropixel probe visualization script

Pull Request - State: closed - Opened by rcpeene almost 3 years ago - 3 comments

#17 - Clean up documentation, environment files and licensing so that we can make Datebook a public repository.

Issue - State: closed - Opened by jeromelecoq almost 3 years ago - 6 comments
Labels: documentation, enhancement

#16 - Small formatting change. Test PR for jupyter notebook viewing

Pull Request - State: closed - Opened by rcpeene almost 3 years ago

#15 - Create notebook to visualize neuronal units coordinate within the mouse brain.

Issue - State: closed - Opened by jeromelecoq almost 3 years ago - 38 comments
Labels: enhancement

#14 - Add jupyternotebook PR visualization to GitHub

Issue - State: closed - Opened by jeromelecoq almost 3 years ago - 5 comments
Labels: documentation, enhancement

#13 - Make book interactive with Thebe

Issue - State: closed - Opened by rcpeene almost 3 years ago - 8 comments
Labels: enhancement