Update getting started guide with v1.0 features

docs/source/getting_started.rst

@@ -8,54 +8,76 @@ This plugin depends on ``ilpy``, which must be installed via conda.::
     conda create -n motile-plugin python=3.10
     conda activate motile-plugin
     conda install -c conda-forge -c funkelab -c gurobi ilpy
-    pip install git+https://github.com/funkelab/motile-napari-plugin.git
+    pip install motile-plugin
 
 If this is successful, you can then run ``napari`` from your command line, and
-the motile plugin should be visible in the "Plugins" drop down menu.
+the motile plugin should be visible in the ``Plugins`` drop down menu.
 Clicking this should open the motile widget on the right of the viewer.
 
 Input data
 ----------
-The motile plugin takes as input expects a Labels layer with time as the
+The motile plugin does not perform detection: you must provide a Labels layer or a Points layer
+containing the objects you want to track.
+The Labels layer must have time as the
 first dimension followed by the spatial dimensions (no channels).
-You can load an example 2D HeLa Dataset from the `Cell Tracking Challenge`_ 
-in "Files" -> "Sample Data".
+You can load an example Labels layer of a 2D HeLa dataset from the `Cell Tracking Challenge`_
+in ``Files`` -> ``Sample Data`` -> ``Fluo-N2DL-HeLa (Motile)``.
+The Points layer must have the point locations with time as the first number,
+followed by the spatial dimensions. While source images are
+nice to qualitatively evaluate results, they are not necessary to run tracking.
 
-In the future, we could also support Points layers as input - please react to 
-`Issue #30`_ if this is important to your use case. While source images are 
-nice to qualitatively evaluate results, they are not necessary to run tracking. 
+In the future, we could also support Shapes layers as input (for example,
+for bounding box tracking) - please react to
+`Issue #48`_ if this is important to your use case, and give feedback on what type
+of shape linking you want.
 
 Running tracking
 ----------------
-The motile plugin by default opens to the "Run Editor" view. In this section,
-you can pick a name for your run, select an input Labels layer, set
+The motile plugin by default opens to the ``Run Editor`` view. In this section,
+you can pick a name for your run, select an input layer, set
 hyperparameters, and start a motile run. Hovering over the title of each
 element in the widget will make a tooltip appear describing the purpose
-of the element. When you are ready, click the "Run" button to start tracking.
+of the element. When you are ready, click the ``Run Tracking`` button to start tracking.
 
 Viewing run results
 -------------------
-Clicking the "Run" button will automatically take you to the "Run Viewer".
-Here you will see:
+Clicking the ``Run Tracking`` button will automatically take you to the ``Run Viewer``.
+It contains the following:
 
-- the solver status
-- a graph of the solver gap (an optimization value that should approach zero)
-- the hyperparameters of the run
-- a button to save the whole run (for persistent viewing in the plugin)
-- a button to export just the tracks as a CSV
-- a button to return to the Run Editor
+- The ``Solver status`` label, which will display if the solver is in progress or
+  done solving.
+- The ``Graph of solver gap``, which is mostly for debugging purposes.
+  The solver gap is an optimization value that should decrease at each iteration.
+- The run settings, including ``Hyperparameters``, ``Costs``, and ``Attribute weights``.
+- The ``Save run`` button. This button will take you to a file dialog to save the
+  whole run, so that if you close napari and re-open it, you can load the run
+  and see the results.
+- The ``Export tracks to CSV`` button, which will take you to a file dialog for saving
+  a csv file containing the tracks. If your input was a Labels layer, the
+  ``node_id`` will be determined by the time and the original segmentation label id.
+  If your input was a Points layer, the ``node_id`` is simply the index of the
+  node in the list of points.
+    - Note: This does not save the output segmentation. If you want to save
+  the relabeled segmentation, you can do so through napari by selecting the
+  layer and then selecting ``File``-> ``Save selected layers``
+- The ``Back to editing`` button, which will return you to the ``Run Editor`` in its
+  previous state.
+- The ``Edit this run`` button. This button will take you back to the ``Run Editor``,
+  but will overwrite the previous settings with the settings of the run you are
+  viewing.
 
-Once the solver completes, you will also see a segmentation and a tracks layer
-in the napari viewer. These are the tracking results.
+Once the solver completes, you will also see a tracks layer
+in the napari viewer. If your input was a segmentation, there will also be
+a new segmentation layer where the IDs have been relabeled to match across time.
 
-A list of "Tracking Runs" will also appear at the bottom of the widget.
+A list of ``Tracking Runs`` will also appear at the bottom of the widget.
 These are the runs that are stored in memory - if you run tracking multiple
 times with different inputs or parameters, you can click back and forth
 between the results here. Deleting runs you do not want to keep viewing
-is a good idea, since these are stored in memory. Runs that were saved in 
-previous sessions do not appear here until you load them from disk with the 
-"Load Run" button.
+is a good idea, since these are stored in memory. Runs that were saved in
+previous sessions do not appear here until you load them from disk with the
+``Load Run`` button.
 
 
-.. _Issue #30: https://github.com/funkelab/motile-napari-plugin/issues/30
-.. _Cell Tracking Challenge: https://celltrackingchallenge.net/
+.. _Issue #48: https://github.com/funkelab/motile_napari_plugin/issues/48
+.. _Cell Tracking Challenge: https://celltrackingchallenge.net/