Ecosyste.ms: Issues

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GitHub / datajoint/element-calcium-imaging issues and pull requests

#194 - fix: robust handling of paths between steps (tables)

Pull Request - State: closed - Opened by ttngu207 6 months ago

#193 - fix: bugfix getting abs path

Pull Request - State: closed - Opened by ttngu207 6 months ago

#192 - Add ROI drawing widget

Pull Request - State: closed - Opened by kushalbakshi 6 months ago

#191 - fix(field_processing): fix key_source to multi-field only

Pull Request - State: closed - Opened by ttngu207 6 months ago

#190 - Minor fix: infer/make output dir and improve key_source

Pull Request - State: closed - Opened by ttngu207 6 months ago

#189 - Add ROI drawing widget for manual curation

Pull Request - State: closed - Opened by kushalbakshi 6 months ago - 1 comment

#188 - Add pytest

Pull Request - State: closed - Opened by ttngu207 7 months ago

#187 - Image processing / segmentation on a per-field basis

Pull Request - State: closed - Opened by ttngu207 7 months ago

#186 - Image processing / segmentation on a per-field basis

Pull Request - State: closed - Opened by ttngu207 7 months ago

#184 - Update element-interface to `staging` branch

Pull Request - State: closed - Opened by kushalbakshi 8 months ago

#183 - Caiman per plane processing

Pull Request - State: closed - Opened by ttngu207 8 months ago

#182 - Fix merge conflict

Pull Request - State: closed - Opened by ttngu207 8 months ago

#181 - pull from main

Pull Request - State: closed - Opened by ttngu207 8 months ago

#180 - Fix - Remove `plane_idx` from `write_single_bigtiff()`

Pull Request - State: closed - Opened by kushalbakshi 8 months ago

#179 - Adding New Acquisition Software, ThorImage

Issue - State: open - Opened by Paschas 8 months ago
Labels: enhancement

#176 - Minor fixes to notebooks

Pull Request - State: closed - Opened by kushalbakshi 9 months ago

#175 - Update tutorial notebook and minor fixes

Pull Request - State: closed - Opened by kushalbakshi 10 months ago

#174 - Add multi-plane processing using CaImAn

Pull Request - State: closed - Opened by kushalbakshi 10 months ago

#173 - revert: :memo: revert docs dark mode cell text color

Pull Request - State: closed - Opened by A-Baji 11 months ago
Labels: bug, documentation

#172 - Revert old `slice` commit

Pull Request - State: closed - Opened by kushalbakshi 12 months ago

#171 - Formatting + Fix typo indicies -> indices

Pull Request - State: closed - Opened by kushalbakshi 12 months ago

#170 - Add motion correction indicies to caiman params

Pull Request - State: closed - Opened by kushalbakshi 12 months ago - 1 comment

#169 - Fix docs - Missing left navigation sidebar

Pull Request - State: closed - Opened by kabilar about 1 year ago
Labels: bug

#168 - Update `mkdocs.yaml` and typo in `setup.py`

Pull Request - State: closed - Opened by MilagrosMarin about 1 year ago

#167 - Hard fix 'force_sktiff' suite2p parameter

Pull Request - State: closed - Opened by sidhulyalkar about 1 year ago

#166 - Fix `PrairieViewMeta` import statements

Pull Request - State: closed - Opened by kushalbakshi about 1 year ago

#165 - bugfix in infer_output_dir

Pull Request - State: closed - Opened by ttngu207 about 1 year ago

#164 - bugfix in `infer_output_dir`

Pull Request - State: closed - Opened by ttngu207 about 1 year ago

#163 - pull from upsteam main

Pull Request - State: closed - Opened by ttngu207 about 1 year ago

#162 - pull from `main`

Pull Request - State: closed - Opened by ttngu207 about 1 year ago

#161 - Per plane processing

Pull Request - State: closed - Opened by ttngu207 about 1 year ago

#160 - Bugfix: rename get_image_files to get_calcium_imaging_files

Pull Request - State: closed - Opened by sidhulyalkar about 1 year ago - 4 comments

#159 - Add z drift metrics to `imaging.py`

Pull Request - State: open - Opened by kushalbakshi about 1 year ago

#158 - Update `get_calcium_imaging_files` and installation instructions

Pull Request - State: closed - Opened by kabilar about 1 year ago

#157 - Update version for release

Pull Request - State: closed - Opened by kabilar about 1 year ago

#156 - Export from DataJoint Element to NWB

Pull Request - State: closed - Opened by kushalbakshi about 1 year ago

#155 - Update import statement for prairie_view_loader

Pull Request - State: closed - Opened by kushalbakshi about 1 year ago - 1 comment

#154 - Update GitHub Actions, Dev Container, and dependencies

Pull Request - State: closed - Opened by kabilar about 1 year ago

#153 - Add license scan report and status

Pull Request - State: closed - Opened by fossabot about 1 year ago - 1 comment

#152 - Update README and Dev Container

Pull Request - State: closed - Opened by kabilar about 1 year ago - 1 comment

#151 - Patch issue with nullable attributes

Pull Request - State: closed - Opened by kabilar over 1 year ago - 1 comment

#150 - Update requirements

Pull Request - State: closed - Opened by kabilar over 1 year ago

#149 - Update Codespace configuration

Pull Request - State: closed - Opened by kabilar over 1 year ago

#148 - Remove requirements

Pull Request - State: closed - Opened by kabilar over 1 year ago - 1 comment

#147 - Remove host requirements

Pull Request - State: closed - Opened by kabilar over 1 year ago - 1 comment

#146 - Fix output of cells in `tutorial` notebook

Pull Request - State: closed - Opened by kabilar over 1 year ago - 1 comment

#145 - Update tutorial notebook

Pull Request - State: closed - Opened by kabilar over 1 year ago - 1 comment

#144 - Fix docs and `get_imaging_root_data_dir` function

Pull Request - State: closed - Opened by kabilar over 1 year ago - 1 comment

#143 - Use `get_session_directory` function

Issue - State: closed - Opened by kabilar about 3 years ago - 1 comment
Labels: enhancement

#142 - Add pytests for trial-based experiments

Issue - State: open - Opened by kabilar almost 3 years ago - 2 comments
Labels: enhancement

#141 - Add pytest for multiple root data directories

Issue - State: open - Opened by kabilar over 2 years ago

#140 - Add an upstream table for `scan.ScanLocation`

Issue - State: open - Opened by CBroz1 over 2 years ago
Labels: bug

#139 - Remove order requirements for `test_pipeline_generation.py`

Issue - State: closed - Opened by CBroz1 over 2 years ago
Labels: bug

#138 - Pytest QOL improvements

Issue - State: open - Opened by CBroz1 over 2 years ago
Labels: enhancement

#137 - Add pytests for CaImAn 2D and 3D datasets

Issue - State: open - Opened by kabilar over 3 years ago
Labels: enhancement

#136 - Add CaImAn, Suite2p, and EXTRACT citations

Pull Request - State: closed - Opened by kabilar over 1 year ago

#135 - Integrate `workflow-calcium-imaging`'s tutorial environment, notebooks, and tests

Pull Request - State: closed - Opened by kabilar over 1 year ago - 1 comment

#134 - Update docs

Pull Request - State: closed - Opened by kabilar over 1 year ago - 1 comment

#133 - Fix dark mode and CI/CD issues

Pull Request - State: closed - Opened by kushalbakshi over 1 year ago

#132 - Fix docs tutorials in dark mode

Pull Request - State: closed - Opened by kushalbakshi over 1 year ago

#131 - Tutorial notebook renders incorrectly in dark mode

Issue - State: closed - Opened by kushalbakshi over 1 year ago - 1 comment

#130 - Add quality metrics

Pull Request - State: closed - Opened by kabilar over 1 year ago - 1 comment

#129 - Update version for element-interface requirement

Pull Request - State: closed - Opened by kushalbakshi over 1 year ago

#128 - New activity

Pull Request - State: closed - Opened by ttngu207 over 1 year ago - 1 comment

#127 - Issue #49

Pull Request - State: closed - Opened by MauryaRitesh over 1 year ago - 2 comments

#126 - Fix bug with docs release

Pull Request - State: closed - Opened by kabilar over 1 year ago - 1 comment

#125 - Add requirement for `ipywidgets`

Pull Request - State: closed - Opened by kushalbakshi over 1 year ago - 1 comment

#124 - Update `requirements.txt` and `scan.py`

Pull Request - State: closed - Opened by virenvarma007 over 1 year ago - 4 comments

#123 - Fix to render images inline

Pull Request - State: closed - Opened by kabilar over 1 year ago - 1 comment

#122 - Update changelog and version for new release

Pull Request - State: closed - Opened by sidhulyalkar over 1 year ago

#121 - fix Tuple ()->[] bug

Pull Request - State: closed - Opened by sidhulyalkar over 1 year ago - 1 comment

#120 - Notebook rendering and linting

Pull Request - State: closed - Opened by CBroz1 over 1 year ago - 6 comments

#119 - Looking for contacts in France

Issue - State: closed - Opened by phanhuynh over 1 year ago - 3 comments

#118 - Update version.py

Pull Request - State: closed - Opened by kushalbakshi over 1 year ago

#117 - Update CHANGELOG

Pull Request - State: closed - Opened by kushalbakshi over 1 year ago

#116 - Fix docs link

Pull Request - State: closed - Opened by kabilar over 1 year ago

#115 - bugfix, detect and infer empty-string outputdir

Pull Request - State: closed - Opened by ttngu207 over 1 year ago

#114 - add caiman processing on interleaved data

Pull Request - State: closed - Opened by tdincer over 1 year ago

#113 - Rearrange requirements installation

Pull Request - State: closed - Opened by tdincer over 1 year ago - 1 comment

#112 - Broken link fix.

Pull Request - State: closed - Opened by tdincer over 1 year ago

#111 - Error fix in `ScanInfo` for PrairieView scans

Pull Request - State: closed - Opened by kushalbakshi over 1 year ago - 5 comments

#110 - bugfix, store output_dir as relative path

Pull Request - State: closed - Opened by ttngu207 over 1 year ago - 4 comments

#109 - Add imports for Bruker PrairieView data

Pull Request - State: closed - Opened by kushalbakshi almost 2 years ago - 2 comments

#108 - Add support to run EXTRACT

Pull Request - State: closed - Opened by tdincer almost 2 years ago - 3 comments

#107 - Add quality metrics

Pull Request - State: closed - Opened by tdincer almost 2 years ago - 9 comments

#106 - add missing "unique index (param_set_hash)"

Pull Request - State: closed - Opened by tdincer almost 2 years ago

#105 - limit TraceReport to the masks with traces

Pull Request - State: closed - Opened by tdincer almost 2 years ago

#104 - bugfix comment

Pull Request - State: closed - Opened by ttngu207 almost 2 years ago

#103 - fix image scaling

Pull Request - State: closed - Opened by tdincer almost 2 years ago

#102 - suite2p - update params with: fs, nplanes, nchannels

Pull Request - State: closed - Opened by ttngu207 almost 2 years ago

#101 - Mkdocs deplpoyment + styling

Pull Request - State: closed - Opened by CBroz1 almost 2 years ago - 2 comments

#100 - bug fix: np.quantile input

Pull Request - State: closed - Opened by tdincer almost 2 years ago

#99 - remove cv2 import

Pull Request - State: closed - Opened by tdincer almost 2 years ago

#98 - parse scan datetime from nd2 files

Pull Request - State: closed - Opened by tdincer almost 2 years ago

#97 - version.py updated for previous merge

Pull Request - State: closed - Opened by kushalbakshi almost 2 years ago

#96 - add plotting package in requirements

Pull Request - State: closed - Opened by tdincer almost 2 years ago

#95 - Documentation

Pull Request - State: closed - Opened by tdincer almost 2 years ago - 1 comment