Merge pull request #888 from TheDeanLab/updated_configuration

Updated configuration

Author: AdvancedImagingUTSW

docs/source/contributing/software_architecture.rst

@@ -6,6 +6,8 @@ Software Architecture
     :align: center
     :alt: Software Architecture
 
+------------------
+
 .. _software-architecture-section:
 
 Model View Controller (MVC)
@@ -26,9 +28,11 @@ The architecture of **navigate** is designed following the industry-standard Mod
   It relays user input in the form of traces and commands to the model and relays model
   output in the form of images and data to the view.
 
+------------------
+
 
-Communication Enhancements
-----------------------------
+Extendability
+============================
 
 To maximize the extendability of **navigate**, it incorporates:
 
@@ -39,8 +43,11 @@ To maximize the extendability of **navigate**, it incorporates:
 - **Plugin Layer**: Offers the flexibility to integrate non-supported devices through
   plugins, enhancing the system's adaptability to various hardware.
 
+------------------
+
+
 Data Acquisition and Processing
---------------------------------
+===============================
 
 **navigate** employs a feature container for running acquisition routines, characterized by:
 
@@ -55,8 +62,11 @@ Data Acquisition and Processing
   **navigate** during run-time. Image analysis is performed on images in memory that are
   stored as numpy arrays, ensuring rapid processing.
 
+------------------
+
+
 Feature Lists
--------------------
+============================
 
 Feature lists are highly versatile, capable of:
 

docs/source/index.rst

@@ -57,7 +57,7 @@ technology developers.
    :caption: User Guide
    :maxdepth: 1
 
-   user_guide/hardware_overview
+   user_guide/hardware/hardware_home
    user_guide/file_formats
    user_guide/gui_walkthrough
    user_guide/setup_microscope

docs/source/user_guide/hardware/camera.rst

@@ -0,0 +1,209 @@
+
+.. _camera_configuration:
+=======
+Cameras
+=======
+
+The software supports camera-based acquisition. It can run both normal and rolling
+shutter modes of contemporary scientific CMOS cameras.
+
+Hamamatsu
+---------
+
+.. note::
+
+    **navigate** has been tested with the following versions of the Hamamatsu's
+    drivers:
+
+    - DCAM API: 20.7.641, 21.7.4321, 22.9.6509, 22.11.4321, 23.12.6736
+    - Camera Firmware: 2.21B, 2.53.A, 3.20.A, 4.30.B,
+    - Active Silicon CoaXpress: 1.10, 1.13, 1.21.
+
+
+-----------------
+
+ORCA-Flash4.0 V3
+~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+-   :ref:`Install Directions <dcam>`.
+-   `ORCA-Flash 4.0 v3 Manual <https://www.hamamatsu
+    .com/us/en/product/cameras/cmos-cameras/C13440-20CU.html>`_.
+
+.. collapse:: Configuration File
+
+    .. code-block:: yaml
+
+      microscopes:
+        microscope_name:
+            camera:
+              hardware:
+                type: HamamatsuOrca
+                serial_number: 111
+                camera_connection:
+              defect_correct_mode: 2.0
+              delay: 1.0  #ms
+              settle_down: 0.1 #ms
+              flip_x: False
+              flip_y: False
+
+
+|
+
+------------------
+
+
+ORCA-Fusion
+~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+-   :ref:`Install Directions <dcam>`.
+-   `ORCA-Fusion Manual <https://www.hamamatsu
+    .com/jp/en/product/cameras/cmos-cameras/C15440-20UP.html>`_.
+
+.. collapse:: Configuration File
+
+    .. code-block:: yaml
+
+      microscopes:
+        microscope_name:
+            camera:
+              hardware:
+                type: HamamatsuOrcaFusion
+                serial_number: 111
+                camera_connection:
+              defect_correct_mode: 2.0
+              delay: 1.0  #ms
+              settle_down: 0.1 #ms
+              flip_x: False
+              flip_y: False
+
+
+|
+
+------------------
+
+
+ORCA-Lightning
+~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+-   :ref:`Install Directions <dcam>`.
+-   `ORCA-Lightning Manual <https://www.hamamatsu
+    .com/us/en/product/cameras/cmos-cameras/C14120-20P.html>`_.
+
+
+.. collapse:: Configuration File
+
+    .. code-block:: yaml
+
+      microscopes:
+        microscope_name:
+            camera:
+              hardware:
+                type: HamamatsuOrcaLightning
+                serial_number: 111
+                camera_connection:
+              defect_correct_mode: 2.0
+              delay: 1.0  #ms
+              settle_down: 0.1 #ms
+              flip_x: False
+              flip_y: False
+
+
+|
+
+------------------
+
+
+ORCA-Fire
+~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+
+-   :ref:`Install Directions <dcam>`.
+-   `ORCA-Fire Manual <https://www.hamamatsu.com/us/en/product/cameras/cmos-cameras/C16240-20UP.html>`_.
+
+
+.. collapse:: Configuration File
+
+    .. code-block:: yaml
+
+      microscopes:
+        microscope_name:
+            camera:
+              hardware:
+                type: HamamatsuOrcaFire
+                serial_number: 111
+                camera_connection:
+              defect_correct_mode: 2.0
+              delay: 1.0  #ms
+              settle_down: 0.1 #ms
+              flip_x: False
+              flip_y: False
+
+|
+
+------------------
+
+Photometrics
+------------
+
+-   :ref:`Install Directions <pvcam>`.
+
+
+.. note::
+
+    **navigate** has been tested with the following versions of the Photometric's
+    drivers:
+
+    - PVCAM: 3.9.13
+
+-----------------
+
+Iris 15
+~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+.. collapse:: Configuration File
+
+    .. code-block:: yaml
+
+      microscopes:
+        microscope_name:
+            camera:
+              hardware:
+                type: Photometrics
+                serial_number: 111
+                camera_connection: PMPCIECam00
+              defect_correct_mode: 2.0
+              delay: 1.0  #ms
+              settle_down: 0.1 #ms
+              flip_x: False
+              flip_y: False
+
+
+|
+
+------------------
+
+
+Synthetic Camera
+----------------
+
+The synthetic camera simulates noise images from an sCMOS camera. If no camera is present,
+the synthetic camera class must be used.
+
+.. collapse:: Configuration File
+
+    .. code-block:: yaml
+
+       microscopes:
+        microscope_name:
+            camera:
+              hardware:
+                type: synthetic
+                serial_number: 111
+                camera_connection:
+              defect_correct_mode: 2.0
+              delay: 1.0  #ms
+              settle_down: 0.1 #ms
+              flip_x: False
+              flip_y: False
+
+|