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2 changes: 1 addition & 1 deletion .github/ISSUE_TEMPLATE/config.yml
Original file line number Diff line number Diff line change
@@ -1,5 +1,5 @@
blank_issues_enabled: false
contact_links:
- name: DataJoint Contribution Guideline
url: https://docs.datajoint.org/python/community/02-Contribute.html
url: https://docs.datajoint.com/about/contribute/
about: Please make sure to review the DataJoint Contribution Guidelines
2 changes: 1 addition & 1 deletion CONTRIBUTING.md
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@@ -1,5 +1,5 @@
# Contribution Guidelines

This project follows the
[DataJoint Contribution Guidelines](https://datajoint.com/docs/about/contribute/).
[DataJoint Contribution Guidelines](https://docs.datajoint.com/about/contribute/).
Please reference the link for more full details.
2 changes: 1 addition & 1 deletion README.md
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Expand Up @@ -37,7 +37,7 @@ environment and notebooks to learn the pipeline.
+ [Interactive tutorial on GitHub
Codespaces](https://github.com/datajoint/element-miniscope#interactive-tutorial)

+ [Documentation](https://datajoint.com/docs/elements/element-miniscope)
+ [Documentation](https://docs.datajoint.com/elements/element-miniscope/)

## Support

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2 changes: 1 addition & 1 deletion docs/mkdocs.yaml
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@@ -1,7 +1,7 @@
# ---------------------- PROJECT SPECIFIC ---------------------------

site_name: DataJoint Documentation
site_url: http://localhost/docs/elements/element-miniscope
site_url: https://docs.datajoint.com/elements/element-miniscope/
repo_url: https://github.com/datajoint/element-miniscope
repo_name: datajoint/element-miniscope
nav:
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7 changes: 3 additions & 4 deletions docs/src/.overrides/partials/nav.html
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Expand Up @@ -7,15 +7,14 @@
{% endif %}
<nav class="{{ class }}" aria-label="{{ lang.t('nav.title') }}" data-md-level="0">
<label class="md-nav__title" for="__drawer">
<a href="{{ config.extra.homepage | d(nav.homepage.url, true) | url }}"
title="{{ config.site_name | e }}" class="md-nav__button md-logo"
aria-label="{{ config.site_name }}" data-md-component="logo">
<a href="{{ config.extra.homepage | d(nav.homepage.url, true) | url }}" title="{{ config.site_name | e }}"
class="md-nav__button md-logo" aria-label="{{ config.site_name }}" data-md-component="logo">
{% include "partials/logo.html" %}
</a>
{#-
Add DataJoint home link to navigation header, otherwise unchanged
-#}
<a href="https://datajoint.com/docs/elements/" title="DataJoint Elements">
<a href="https://docs.datajoint.com/elements/" title="DataJoint Elements">
⬅ Home
</a>
</label>
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10 changes: 3 additions & 7 deletions docs/src/pipeline.md
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Expand Up @@ -11,7 +11,7 @@ detailed documentation on each table, see the API docs for the respective schema

### `reference` schema

+ For further details see the [reference schema API docs](https://datajoint.com/docs/elements/element-miniscope/latest/api/workflow_miniscope/reference/)
+ For further details see the [reference schema API docs](https://docs.datajoint.com/elements/element-miniscope/0.3/api/workflow_miniscope/reference/)

| Table | Description |
| --- | --- |
Expand All @@ -21,15 +21,15 @@ detailed documentation on each table, see the API docs for the respective schema

+ Although not required, most choose to connect the `Session` table to a `Subject` table.

+ For further details see the [subject schema API docs](https://datajoint.com/docs/elements/element-animal/api/element_animal/subject/)
+ For further details see the [subject schema API docs](https://docs.datajoint.com/elements/element-animal/latest/api/element_animal/subject/)

| Table | Description |
| --- | --- |
| Subject | Basic information of the research subject. |

### `session` schema

+ For further details see the [session schema API docs](https://datajoint.com/docs/elements/element-session/latest/api/element_session/session_with_datetime/)
+ For further details see the [session schema API docs](https://docs.datajoint.com/elements/element-session/latest/api/element_session/session_with_datetime/)

| Table | Description |
| --- | --- |
Expand All @@ -39,8 +39,6 @@ detailed documentation on each table, see the API docs for the respective schema

+ Tables related to importing and analyzing miniscope data.

+ For further details see the [miniscope schema API docs](https://datajoint.com/docs/elements/element-miniscope/latest/api/element_miniscope/miniscope)

| Table | Description |
| --- | --- |
| AcquisitionSoftware | Software used for miniscope acquisition |
Expand Down Expand Up @@ -78,8 +76,6 @@ detailed documentation on each table, see the API docs for the respective schema

+ Tables that provide summary reports of the processed miniscope data.

+ For further details see the [miniscope_report API docs](https://datajoint.com/docs/elements/element-miniscope/latest/api/element_miniscope/miniscope_report)

| Table | Description |
| --- | --- |
| QualityMetrics | A table containing information about CaImAn estimates: </p> + `r_values`: Space correlation </p> + `snr`: Trace SNR </p> + `cnn_preds`: CNN predictions|
2 changes: 1 addition & 1 deletion docs/src/tutorials/index.md
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Expand Up @@ -13,7 +13,7 @@
+ The Workflow Miniscope described above can be modified for a user's specific experimental requirements and thereby used in active projects.

+ The GitHub Codespace and Dev Container is configured for tutorials and prototyping.
We recommend users to configure a database specifically for production pipelines. Instructions for a local installation of the integrated development environment with a database can be found on the [User Guide](https://datajoint.com/docs/elements/user-guide/) page.
We recommend users to configure a database specifically for production pipelines. Instructions for a local installation of the integrated development environment with a database can be found on the [User Guide](https://docs.datajoint.com/elements/user-guide/) page.

## Videos

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