diff --git a/openflexure_microscope/api/app.py b/openflexure_microscope/api/app.py
index 8a237e73..8c991be5 100644
--- a/openflexure_microscope/api/app.py
+++ b/openflexure_microscope/api/app.py
@@ -29,7 +29,7 @@ from labthings import create_app
 from labthings.extensions import find_extensions
 from labthings.views import View
 
-from openflexure_microscope.api.microscope import default_microscope as api_microscope
+from openflexure_microscope.microscope import Microscope
 from openflexure_microscope.api.utilities import init_default_extensions, list_routes
 from openflexure_microscope.api.v2 import views
 from openflexure_microscope.json import JSONEncoder
@@ -39,11 +39,7 @@ from openflexure_microscope.paths import (
     logs_file_path,
 )
 
-# Handle logging
-access_log = logging.getLogger("werkzeug")
-# Block the access logs from propagating up to the root logger
-access_log.propagate = False
-
+# Log files
 ROOT_LOGFILE = logs_file_path("openflexure_microscope.log")
 ACCESS_LOGFILE = logs_file_path("openflexure_microscope.access.log")
 
@@ -52,8 +48,12 @@ formatter = logging.Formatter(
     "[%(asctime)s] [%(threadName)s] [%(levelname)s] %(message)s"
 )
 
+# Our WSGI server uses Werkzeug, so use that for the access log
+access_log = logging.getLogger("werkzeug")
+# Block the access logs from propagating up to the root logger
+access_log.propagate = False
 
-# Create file handler
+# Create error log file handler
 fh = logging.handlers.RotatingFileHandler(
     ROOT_LOGFILE, maxBytes=1_000_000, backupCount=5
 )
@@ -76,8 +76,14 @@ access_log.addHandler(afh)
 # Log server paths being used
 logging.info("Running with data path %s", OPENFLEXURE_VAR_PATH)
 
-logging.info("Creating app")
+# Create the microscope object
+api_microscope = Microscope()
+logging.debug("Restoring captures...")
+api_microscope.captures.rebuild_captures()
+logging.debug("Microscope successfully attached!")
+
 # Create flask app
+logging.info("Creating app")
 app, labthing = create_app(
     __name__,
     prefix="/api/v2",
@@ -95,7 +101,7 @@ cors = CORS(app)
 labthing.json_encoder = JSONEncoder
 app.json_encoder = JSONEncoder
 
-# Attach lab devices
+# Add the microscope object to LabThings so extensions can access it
 labthing.add_component(api_microscope, "org.openflexure.microscope")
 
 # Attach extensions
@@ -129,7 +135,6 @@ labthing.add_root_link(views.ConfigurationProperty, "instrumentConfiguration")
 # Attach stage resources
 labthing.add_view(views.StageTypeProperty, "/instrument/stage/type")
 
-
 # Attach streams resources
 labthing.add_view(views.MjpegStream, "/streams/mjpeg")
 labthing.add_view(views.SnapshotStream, "/streams/snapshot")
@@ -142,7 +147,7 @@ for name, action in views.enabled_root_actions().items():
     rule = action["rule"]
     labthing.add_view(view_class, f"/actions{rule}")
 
-# Add log file view
+# Add log file download view
 class LogFileView(View):
     def get(self):
         """
diff --git a/openflexure_microscope/api/microscope.py b/openflexure_microscope/api/microscope.py
deleted file mode 100644
index 79bada52..00000000
--- a/openflexure_microscope/api/microscope.py
+++ /dev/null
@@ -1,11 +0,0 @@
-import logging
-
-from openflexure_microscope.microscope import Microscope
-
-default_microscope = Microscope()
-
-# Restore loaded capture array to camera object
-logging.debug("Restoring captures...")
-default_microscope.captures.rebuild_captures()
-
-logging.debug("Microscope successfully attached!")