Merge pull request #52 from kabilar/calcium

Update to merge `workflow-calcium-imaging` into `element-calcium-imaging`

Author: dimitri-yatsenko

src/community/partnership-suite2p.md

@@ -86,13 +86,13 @@ and Suite2p.
 [Element Calcium Imaging](https://github.com/datajoint/element-calcium-imaging/blob/00df4434fcfd6c1497d7950601248f046170139e/element_calcium_imaging/imaging.py#L267-L299)
 
 - [x] Tutorials on running DataJoint Element with Suite2p - 
-[Workflow Calcium Imaging Jupyter notebooks](https://github.com/datajoint/workflow-calcium-imaging/tree/main/notebooks)
+[Element Calcium Imaging Jupyter notebooks](https://github.com/datajoint/element-calcium-imaging/tree/main/notebooks)
 
 - [x] Tests to verify loading Suite2p data - 
-[Pytests](https://github.com/datajoint/workflow-calcium-imaging/blob/main/tests/test_populate.py)
+[Pytests](https://github.com/datajoint/element-calcium-imaging/blob/main/tests/test_populate.py)
 
 - [x] Tests to verify running Suite2p - 
-[Pytests](https://github.com/datajoint/workflow-calcium-imaging/blob/main/tests/test_populate.py)
+[Pytests](https://github.com/datajoint/element-calcium-imaging/blob/main/tests/test_populate.py)
 
 ## Citation
 

src/elements/concepts.md

@@ -94,5 +94,5 @@ For instance, the
 [Scan module](https://github.com/datajoint/element-calcium-imaging/blob/main/element_calcium_imaging/scan.py)
 receives its required functions from the linking module passed into the module's
 `activate` function. See the 
-[corresponding workflow](https://github.com/datajoint/workflow-calcium-imaging/)
+[example notebooks](https://github.com/datajoint/element-calcium-imaging/)
 for an example of how the linking module is passed into the Element's module.

src/elements/index.md

@@ -24,7 +24,7 @@ Below are the projects that make up the family of open-source DataJoint Elements
     A data pipeline for calcium imaging microscopy.
 
     [:octicons-arrow-right-24: Interactive tutorial on GitHub
-    Codespaces](https://github.com/datajoint/workflow-calcium-imaging#interactive-tutorial){:target="_blank"}
+    Codespaces](https://github.com/datajoint/element-calcium-imaging#interactive-tutorial){:target="_blank"}
 
     [:octicons-arrow-right-24: Docs](./element-calcium-imaging/)
 

src/elements/management/dissemination.md

@@ -15,7 +15,7 @@ neuroscience labs. These activities include
   - [DataJoint Tutorials](https://github.com/datajoint/datajoint-tutorials)
   - [DataJoint Workflow Array
     Ephys](https://github.com/datajoint/workflow-array-ephys#interactive-tutorial)
-  - [DataJoint Workflow Calcium Imaging](https://github.com/datajoint/workflow-calcium-imaging#interactive-tutorial)
+  - [DataJoint Element Calcium Imaging](https://github.com/datajoint/element-calcium-imaging#interactive-tutorial)
 
 ## 2. Community Survey
 

src/elements/user-guide.md

@@ -259,7 +259,7 @@ needs.
 
     An example workflow for calcium imaging microscopy.
 
-    [:octicons-repo-forked-24: Clone from GitHub](https://github.com/datajoint/workflow-calcium-imaging/)
+    [:octicons-repo-forked-24: Clone from GitHub](https://github.com/datajoint/element-calcium-imaging/)
 
 -   :fontawesome-brands-python:{ .lg .middle } **Workflow Miniscope**
 
@@ -481,12 +481,12 @@ organized, and how some files are named.
         
     - The `subject` directory names must match the subject IDs in your subjects table. 
         The `ingest.py` script (
-        [demo ingestion notebook](https://github.com/datajoint/workflow-calcium-imaging/blob/main/notebooks/04-automate-optional.ipynb)
+        [tutorial notebook](https://github.com/datajoint/element-calcium-imaging/blob/main/notebooks/tutorial.ipynb)
         ) can help load these values from `./user_data/subjects.csv`.
 
     - The `session` directories can have any naming convention, but must be specified 
         in the session table (see also
-        [demo ingestion notebook])(https://github.com/datajoint/workflow-calcium-imaging/blob/main/notebooks/04-automate-optional.ipynb)
+        [tutorial notebook])(https://github.com/datajoint/element-calcium-imaging/blob/main/notebooks/tutorial.ipynb)
         . 
 
     - Each `session` directory should contain:

src/index.md

@@ -1,5 +1,7 @@
 # Welcome to the DataJoint Documentation
 
+![pipeline](https://raw.githubusercontent.com/datajoint/datajoint-python/master/images/pipeline.png){: style="height:300px;"}
+
 <h2> DataJoint Ecosystem </h2>
 
 <div class="grid cards" markdown>