diff --git a/docs/requirements.txt b/docs/requirements.txt
index 6ba8bc78..9aa2c29a 100644
--- a/docs/requirements.txt
+++ b/docs/requirements.txt
@@ -1 +1,2 @@
-sphinxcontrib.httpdomain
\ No newline at end of file
+sphinxcontrib.httpdomain
+sphinx_rtd_theme
\ No newline at end of file
diff --git a/docs/source/apirequests.rst b/docs/source/apirequests.rst
index e828614b..2c836c15 100644
--- a/docs/source/apirequests.rst
+++ b/docs/source/apirequests.rst
@@ -42,21 +42,23 @@ CURL
 .. code-block:: none
 
    curl -X POST -H "Content-Type: application/json" -d \\
-   '{"picamera_settings": {"shutter_speed": 2000}, "jpeg_quality": 90}' http://192.168.1.126:5000/api/v1/config
+   '{"camera_settings": {"picamera_settings": {"shutter_speed": 2000}, "jpeg_quality": 90}}' http://192.168.1.126:5000/api/v1/config
 
 HTTPie
 ++++++
 .. code-block:: none
 
-   http POST http://192.168.1.126:5000/api/v1/config jpeg_quality:=90 picamera_settings:='{"shutter_speed": 2000}'
+   http POST http://192.168.1.126:5000/api/v1/config camera_settings:='{"jpeg_quality": 90, "picamera_settings": {"shutter_speed": 2000}}' 
 
 Python Requests
 +++++++++++++++
 .. code-block:: python
 
    json_payload = {
-        "jpeg_quality": 90,
-        "picamera_settings": {"shutter_speed": 2000}
+       camera_settings: {
+            "jpeg_quality": 90,
+            "picamera_settings": {"shutter_speed": 2000}
+        }
    }
    requests.post('http://192.168.1.126:5000/api/v1/config', json=json_payload)
 
diff --git a/docs/source/config.rst b/docs/source/config.rst
index 2444e860..9ddbde71 100644
--- a/docs/source/config.rst
+++ b/docs/source/config.rst
@@ -1,5 +1,5 @@
 Microscope configuration
-=======================================================
+========================
 
 .. toctree::
    :maxdepth: 2
@@ -18,7 +18,7 @@ in separate "auxillary" config files, and are linked together by adding the conf
 microscope RC file. This is set up by default, as shown below:
 
 Default microscope_settings.yaml
-+++++++++++++++++++++++++
+++++++++++++++++++++++++++++++++
 .. code-block:: yaml
 
     # Resolutions for streaming and capture
@@ -58,7 +58,7 @@ Example picamera_settings.yaml
 
 
 Loading the runtime-config
-+++++++
+++++++++++++++++++++++++++
 
 By default, a microscope object will load the a runtime-config from the default location.
 This RC can then be passed to any hardware attached to the microscope. This can be particularly
diff --git a/docs/source/plugins/class.rst b/docs/source/plugins/class.rst
index 87366775..205a7071 100644
--- a/docs/source/plugins/class.rst
+++ b/docs/source/plugins/class.rst
@@ -22,12 +22,17 @@ Lock module
 Default plugins
 ---------------
 
-Microscope plugin
-+++++++++++++++++
-.. automodule:: openflexure_microscope.plugins.default.plugin
+Autofocus
++++++++++
+.. automodule:: openflexure_microscope.plugins.default.autofocus
     :members:
 
-Web API plugin
-++++++++++++++
-.. automodule:: openflexure_microscope.plugins.default.api
+Camera calibration
+++++++++++++++++++
+.. automodule:: openflexure_microscope.plugins.default.camera_calibration
     :members:
+
+Scan and Stack
+++++++++++++++
+.. automodule:: openflexure_microscope.plugins.default.scan
+    :members:
\ No newline at end of file
diff --git a/docs/source/plugins/introduction.rst b/docs/source/plugins/introduction.rst
index 36b8e54d..50d163fb 100644
--- a/docs/source/plugins/introduction.rst
+++ b/docs/source/plugins/introduction.rst
@@ -26,7 +26,7 @@ Generally, for adding anything other than very simple functionality, plugins sho
 The main restriction is that the plugin package must be importable using an absolute import from within the Python environment being used to load your microscope. 
 
 Loading plugins with microscope_settings.yaml
---------------------------------------
+---------------------------------------------
 Both types of plugin are loaded by specifying the plugin class in your :ref:`MicroscopeRC`. In the case of a single-file plugin, specify the path to the plugin file, followed by the name of your :py:class:`openflexure_microscope.plugins.MicroscopePlugin` child class, separated by a colon. For packaged plugins, specify the absolute module name in place of the path.
 
 For example, the plugins section of your microscope_settings.yaml file may look like:
diff --git a/openflexure_microscope/api/app.py b/openflexure_microscope/api/app.py
index d2931aa5..44e99e7a 100644
--- a/openflexure_microscope/api/app.py
+++ b/openflexure_microscope/api/app.py
@@ -148,6 +148,12 @@ app.register_blueprint(task_blueprint, url_prefix=uri('/task', 'v1'))
 def routes():
     """
     List of all connected API routes
+
+    .. :quickref: System; Routes
+
+    :>header Accept: application/json
+    :>header Content-Type: application/json
+    :status 200: stream active
     """
     return jsonify(list_routes(app))
 
@@ -156,6 +162,12 @@ def routes():
 def err_log():
     """
     Most recent 1mb of log output
+
+    .. :quickref: System; Log
+
+    :>header Accept: application/json
+    :>header Content-Type: application/json
+    :status 200: stream active
     """
     timestamp = datetime.now().strftime("%Y-%m-%d_%H-%M-%S")
     return send_file(
diff --git a/openflexure_microscope/api/v1/blueprints/base.py b/openflexure_microscope/api/v1/blueprints/base.py
index 2195a025..24681f0d 100644
--- a/openflexure_microscope/api/v1/blueprints/base.py
+++ b/openflexure_microscope/api/v1/blueprints/base.py
@@ -100,35 +100,36 @@ class ConfigAPI(MicroscopeView):
           Content-Type: application/json
 
           {
-            "image_resolution": [
-                2592, 
-                1944
-            ], 
-            "jpeg_quality": 75, 
-            "name": "0e2c6fac5421429aac67c7903107bdd8", 
-            "numpy_resolution": [
-                1312, 
-                976
-            ], 
-            "picamera_settings": {
-                "analog_gain": 1.0, 
-                "digital_gain": 1.0, 
-                "awb_gains": [
-                0.92578125, 
-                2.94921875
-                ], 
-                "awb_mode": "off", 
-                "exposure_mode": "off", 
-                "framerate": 24.0, 
-                "saturation": 0, 
-                "shutter_speed": 5378
-            }, 
+            "id": "0e2c6fac5421429aac67c7903107bdd8", 
+            "name": "docuscope-2000",
+            "fov": [4100, 3146],
+            "camera_settings": {
+                "image_resolution": [2592, 1944], 
+                "numpy_resolution": [1312, 976], 
+                "video_resolution": [832, 624],
+                "jpeg_quality": 75, 
+                "picamera_settings": {
+                    "analog_gain": 1.0, 
+                    "digital_gain": 1.0, 
+                    "awb_gains": [0.92578125, 2.94921875], 
+                    "awb_mode": "off", 
+                    "exposure_mode": "off", 
+                    "framerate": 24.0, 
+                    "saturation": 0, 
+                    "shutter_speed": 5378
+                }, 
+            },
+            "stage_settings": {
+                "backlash": {
+                    "x": 256,
+                    "y": 256,
+                    "z": 0
+                }
+            }
             "plugins": [
-                "openflexure_microscope.plugins.default:Plugin"
-            ], 
-            "stream_resolution": [
-                832, 
-                624
+                "openflexure_microscope.plugins.default.autofocus:AutofocusPlugin",
+                "openflexure_microscope.plugins.default.scan:ScanPlugin",
+                "openflexure_microscope.plugins.default.camera_calibration:Plugin"
             ]
           }
 
@@ -152,18 +153,52 @@ class ConfigAPI(MicroscopeView):
           Accept: application/json
 
           {
-            "analog_gain": 1.0, 
-            "digital_gain": 1.0, 
-            "jpeg_quality": 75, 
-            "picamera_params": {
-                "framerate": 24.0, 
-                "saturation": 0, 
-                "shutter_speed": 5000
+            "id": "0e2c6fac5421429aac67c7903107bdd8", 
+            "name": "docuscope-2000",
+            "fov": [4100, 3146],
+            "camera_settings": {
+                "image_resolution": [2592, 1944], 
+                "numpy_resolution": [1312, 976], 
+                "video_resolution": [832, 624],
+                "jpeg_quality": 75, 
+                "picamera_settings": {
+                    "analog_gain": 1.0, 
+                    "digital_gain": 1.0, 
+                    "awb_gains": [0.92578125, 2.94921875], 
+                    "awb_mode": "off", 
+                    "exposure_mode": "off", 
+                    "framerate": 24.0, 
+                    "saturation": 0, 
+                    "shutter_speed": 5378
+                }, 
+            },
+            "stage_settings": {
+                "backlash": {
+                    "x": 256,
+                    "y": 256,
+                    "z": 0
+                }
             }
+            "plugins": [
+                "openflexure_microscope.plugins.default.autofocus:AutofocusPlugin",
+                "openflexure_microscope.plugins.default.scan:ScanPlugin",
+                "openflexure_microscope.plugins.default.camera_calibration:Plugin"
+            ]
           }
 
         :>header Accept: application/json
 
+        :<json string id: Unique string identifier of the microscope.
+        :<json string name: Friendly name for the microscope
+        :<json array fov: Field of view (motor steps per full width and height of frame)
+        :<json json camera_settings:    - **image_resolution** *(array)*: Resolution of full image captures
+                                        - **numpy_resolution** *(array)*: Resolution of full numpy array captures
+                                        - **video_resolution** *(array)*: Resolution of video recordings, low res image captures, and the preview stream
+                                        - **jpeg_quality** *(int)*: Quality in which to store JPEG capture data
+                                        - **picamera_settings** *(json)*: Key-value pairs to apply directly to any attached PiCamera object
+        :<json json stage_settings:     - **backlash** *(json)*: x, y, and z backlash compensation, in motor steps
+        :<json array plugins: Array of plugin paths to load. Requires reloading the microscope object after applying
+
         :<header Content-Type: application/json
         :status 200: capture created
 
diff --git a/openflexure_microscope/microscope.py b/openflexure_microscope/microscope.py
index 81a447ea..9682059e 100644
--- a/openflexure_microscope/microscope.py
+++ b/openflexure_microscope/microscope.py
@@ -6,9 +6,9 @@ import logging
 import pkg_resources
 import uuid
 
-from openflexure_stage import OpenFlexureStage
+from .stage.base import BaseStage
 
-from .camera.pi import StreamingCamera
+from .camera.base import BaseCamera
 
 from .plugins import PluginMount
 from .utilities import axes_to_array
@@ -28,8 +28,8 @@ class Microscope:
             automatically created if None.
         lock (:py:class:`openflexure_microscope.lock.CompositeLock`): Composite lock controlling thread access
             to multiple pieces of hardware.
-        camera (:py:class:`openflexure_microscope.camera.pi.StreamingCamera`): Camera object
-        stage (:py:class:`openflexure_stage.stage.OpenFlexureStage`): Stage object
+        camera (:py:class:`openflexure_microscope.camera.base.BaseCamera`): Camera object
+        stage (:py:class:`openflexure_microscope.stage.base.BaseStage`): Stage object
         task: (:py:class:`openflexure_microscope.task.TaskOrchestrator`): Threaded ask orchestrator for managing
             background tasks using microscope hardware
         plugin (:py:class:`openflexure_microscope.plugins.PluginMount`): Mounting point for all microscope plugins
@@ -76,7 +76,7 @@ class Microscope:
             self.stage.close()
         logging.info("Closed {}".format(self))
 
-    def attach(self, camera: StreamingCamera, stage: OpenFlexureStage):
+    def attach(self, camera: BaseCamera, stage: BaseStage):
         """
         Retroactively attaches a camera and stage to the microscope object.
 
@@ -84,8 +84,8 @@ class Microscope:
         opened at a later time.
 
         Args:
-            camera (:py:class:`openflexure_microscope.camera.pi.StreamingCamera`): camera object
-            stage (:py:class:`openflexure_stage.stage.OpenFlexureStage`): stage object
+            camera (:py:class:`openflexure_microscope.camera.base.BaseCamera`): camera object
+            stage (:py:class:`openflexure_microscope.stage.base.BaseStage`): stage object
         """
 
         settings_full = self.read_config()
@@ -94,7 +94,7 @@ class Microscope:
         # Maybe even attach dummy hardware at __init__, and replace with real hardware if it exists
 
         logging.debug("Attaching camera...")
-        self.camera = camera  #: :py:class:`openflexure_microscope.camera.pi.StreamingCamera`: Picamera object
+        self.camera = camera  #: :py:class:`openflexure_microscope.camera.base.BaseCamera`: Picamera object
         if not self.camera:
             logging.info("No camera attached.")
         else:
@@ -106,7 +106,7 @@ class Microscope:
                 self.lock.locks.append(self.camera.lock)
 
         logging.debug("Attaching stage...")
-        self.stage = stage  #: :py:class:`openflexure_stage.stage.OpenFlexureStage`: OpenFlexure stage object
+        self.stage = stage  #: :py:class:`openflexure_microscope.stage.base.BaseStage`: OpenFlexure stage object
         if not self.stage:
             logging.info("No stage attached.")
         else:
diff --git a/openflexure_microscope/plugins/default/autofocus/__init__.py b/openflexure_microscope/plugins/default/autofocus/__init__.py
index b88ad3f3..63a64300 100644
--- a/openflexure_microscope/plugins/default/autofocus/__init__.py
+++ b/openflexure_microscope/plugins/default/autofocus/__init__.py
@@ -1 +1,2 @@
+__all__ = ['AutofocusPlugin']
 from .plugin import AutofocusPlugin
\ No newline at end of file
diff --git a/openflexure_microscope/plugins/default/autofocus/plugin.py b/openflexure_microscope/plugins/default/autofocus/plugin.py
index dfc3e612..302fe9a0 100644
--- a/openflexure_microscope/plugins/default/autofocus/plugin.py
+++ b/openflexure_microscope/plugins/default/autofocus/plugin.py
@@ -89,28 +89,36 @@ class AutofocusPlugin(MicroscopePlugin):
 
         This autofocus method is very efficient, as it only passes the peak once.
         The sequence of moves it performs is:
-        1. Move to the top of the range `dz/2` (can be disabled)
-        2. Move down by `dz` while monitoring JPEG size to find the focus.
-        3. Move back up to the `target_z` position, relative to the sharpest image.
-        4. Measure the sharpness, and compare against the curve recorded in (2) to 
-           estimate how much further we need to go.  Make this move, to reach our
-           target position.
+
+        1.  Move to the top of the range `dz/2` (can be disabled)
+
+        2.  Move down by `dz` while monitoring JPEG size to find the focus.
+
+        3.  Move back up to the `target_z` position, relative to the sharpest image.
+
+        4.  Measure the sharpness, and compare against the curve recorded in (2) to \\
+            estimate how much further we need to go.  Make this move, to reach our \\
+            target position.
+
         Moving back to the target position in two steps allows us to correct for
         backlash, by using the sharpness-vs-z curve as a rough encoder for Z.
 
         Parameters:
-        dz: number of steps over which to scan (optional, default 2000)
-        target_z: we aim to finish at this position, relative to focus.  This may
-           be useful if, for example, you want to acquire a stack of images in Z.
-           It is optional, and the default value of 0 will finish at the focus.
-        initial_move_up: (optional, default True) set this to `False` to move down
-           from the starting position.  Mostly useful if you're able to combine
-           the initial move with something else, e.g. moving to the next scan point.
-        mini_backlash: (optional, default 50) is a small extra move made in step
-           3 to help counteract backlash.  It should be small enough that you
-           would always expect there to be greater backlash than this.  Too small
-           might slightly hurt accuracy, but is unlikely to be a big issue.  Too big
-           may cause you to overshoot, which is a problem.
+            dz: number of steps over which to scan (optional, default 2000)
+
+            target_z: we aim to finish at this position, relative to focus.  This may 
+                be useful if, for example, you want to acquire a stack of images in Z. 
+                It is optional, and the default value of 0 will finish at the focus.
+
+            initial_move_up: (optional, default True) set this to `False` to move down
+                from the starting position.  Mostly useful if you're able to combine
+                the initial move with something else, e.g. moving to the next scan point.
+
+            mini_backlash: (optional, default 50) is a small extra move made in step
+                3 to help counteract backlash.  It should be small enough that you
+                would always expect there to be greater backlash than this.  Too small
+                might slightly hurt accuracy, but is unlikely to be a big issue.  Too big
+                may cause you to overshoot, which is a problem.
         """
         with self.monitor_sharpness() as m, self.microscope.camera.lock:
             # Ensure the MJPEG stream has started
diff --git a/openflexure_microscope/plugins/default/camera_calibration/__init__.py b/openflexure_microscope/plugins/default/camera_calibration/__init__.py
index 35c21bdc..0f02ba77 100644
--- a/openflexure_microscope/plugins/default/camera_calibration/__init__.py
+++ b/openflexure_microscope/plugins/default/camera_calibration/__init__.py
@@ -1 +1,2 @@
+__all__ = ['Plugin']
 from .plugin import Plugin
diff --git a/openflexure_microscope/plugins/default/scan/__init__.py b/openflexure_microscope/plugins/default/scan/__init__.py
index d1e1d942..cfdd7ee4 100644
--- a/openflexure_microscope/plugins/default/scan/__init__.py
+++ b/openflexure_microscope/plugins/default/scan/__init__.py
@@ -1 +1,2 @@
+__all__ = ['ScanPlugin']
 from .plugin import ScanPlugin