Merge pull request #1144 from TrungNguyenDuc/Add-stage-for-Newport-Slit-and-Newport-300-mm-stage

Add stage for newport slit and newport 300 mm stage

Author: AdvancedImagingUTSW

docs/source/02_user_guide/01_supported_hardware/camera.rst

@@ -180,6 +180,7 @@ Iris 15
 Ximea
 --------------------------------
 
+
 MU196MR-ON
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~
 
@@ -191,16 +192,32 @@ MU196MR-ON
         microscope_name:
             camera:
               hardware:
-                type: ximea
+                type: ximea.MU196XR
                 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
-
-
+              gain: 1
+              pixel_size_in_microns: 1.4
+              readout_port: 0
+              readout_speed: 1.0
+              settle_down: 0.0
+              speed_table_index: 0
+              supported_readout_directions: ['Top-to-Bottom']
+              supported_sensor_modes: ['Normal']
+              supported_trigger_sources: ['External']
+              trigger_active: 1.0
+              trigger_mode: 1.0
+              trigger_polarity: 2.0
+              trigger_source: 2.0
+              x_pixels: 5112
+              x_pixels_min: 192
+              x_pixels_step: 24
+              y_pixels: 3840
+              y_pixels_min: 2
+              y_pixels_step: 2
 |
 
 ------------------

docs/source/02_user_guide/01_supported_hardware/stage.rst

@@ -2,17 +2,10 @@
 Stages
 ======
 
-Our software empowers users with a flexible solution for configuring
-multiple stages, catering to diverse microscope modalities. Each stage can be
-customized to suit the specific requirements of a particular modality or shared
-across  various modalities. Our unique approach allows seamless integration of stages
-from different manufacturers, enabling users to mix and match components for a truly
-versatile and optimized setup tailored to their research needs.
+Our software empowers users with a flexible solution for configuring multiple stages, catering to diverse microscope modalities. Each stage can be customized to suit the specific requirements of a particular modality or shared across  various modalities. Our unique approach allows seamless integration of stages from different manufacturers, enabling users to mix and match components for a truly versatile and optimized setup tailored to their research needs.
 
 .. Note::
-    The software provides configure specific hardware axes to software axes. This is
-    specified in the configuration file. For example, if specified as follows, the software
-    x, y, z, and f axes can be mapped to the hardware axes M, Y, X, and Z, respectively.
+    The software provides configure specific hardware axes to software axes. This is specified in the configuration file. For example, if specified as follows, the software x, y, z, and f axes can be mapped to the hardware axes M, Y, X, and Z, respectively.
 
     .. code-block:: yaml
 
@@ -586,6 +579,65 @@ identical. The voltage signal is delivered via the data acquisition card specifi
 
 ----------------
 
+
+Newport
+-------
+Newport offers motion control solutions for various applications in microscopy. Our software supports two Newport stage controllers that provide accurate positioning capabilities.
+
+Conex Controller
+~~~~~~~~~~~~~~~~
+
+The Newport Conex Controller series offers compact, integrated motion control solutions that come pre-wired with dedicated controllers for quick, out-of-the-box operation. While the Conex series offers four `different controller types with various drive technologies <https://www.newport.com/c/controller-&-stage-kits>`_, we have used it to drive a `TRA6CC <https://www.newport.com/p/TRA6CC>`_ (Linear Actuator, DC Servo, 6 mm Travel, TRA6CC and CONEX-CC Controller) connected to a `M-SV-0.5 <https://www.newport.com/p/M-SV-0.5>`_ adjustable width slit that is positioned conjugate to the back pupil of the illumination objective. This setup allows precise and automated control of the illumination numerical aperture.
+
+. collapse:: Configuration File
+
+    .. code-block:: yaml
+
+      microscopes:
+        microscope_name:
+            stage:
+              hardware:
+                -
+                  name: slit
+                  type: conex.ConexStage
+                  serial_number: 126
+                  port: COM4
+                  axes: [S]
+                  axes_mapping: [S]
+                      s_min: -10000.0
+                      s_max: 10000.0
+                      s_offset: 0.0
+
+|
+
+--------------
+
+ESP302 Motion Controller Controller
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+The Newport `ESP302 Motion Controller <https://www.newport.com/f/esp30x-3-axis-dc-and-stepper-motion-controller>`_ is a versatile, 1-, 2-, or 3-axis motion controller that provides precise positioning capabilities for a wide range of Newport stages.
+
+. collapse:: Configuration File
+
+    .. code-block:: yaml
+
+      microscopes:
+        microscope_name:
+            stage:
+              hardware:
+                -
+                  name: delay_stage
+                  type: newport.NewportStage
+                  serial_number: 127
+                  axes: [theta]
+                  axes_mapping: [1]
+                  port: "192.168.1.90"
+                  baudrate: 5001
+                  timeout: 5.0
+|
+
+---------------
+
 Synthetic Stage
 ---------------
 If no stage is present for a particular axis, one must configure the software to use a synthetic

src/navigate/config/configuration_database.py

@@ -4,6 +4,7 @@
     "Hamamatsu ORCA Fusion": ("HamamatsuOrcaFusion", "hamamatsu"),
     "Hamamatsu Flash 4.0": ("HamamatsuOrca", "hamamatsu"),
     "Photometrics Iris 15B": ("Photometrics", "photometrics"),
+    "Ximea MU196MR-ON": ("MU196XR", "ximea"),
     "Virtual Device": ("Synthetic", "synthetic"),
 }
 
@@ -172,8 +173,10 @@
     "Applied Scientific Instrumentation": ("ASI", "asi"),
     "ASI MFC2000": ("MFC2000", "asi"),
     "ASI MS2000": ("MS2000", "asi"),
-    "Analog/Digital Device": ("NI", "ni"),
+    "NI Analog/Digital Device": ("NI", "ni"),
+    "Newport Conex Controller": ("Conex", "conex"),
     "Mad City Labs": ("MCL", "mcl"),
+    "Newport ESP302 Motion Controller": ("Newport", "newport"),
     "Physik Instrumente": ("PI", "pi"),
     "Sutter Instruments": ("MP285", "sutter"),
     "ThorLabs KCube Inertial Device KIM001": ("KIM001", "thorlabs"),
@@ -469,7 +472,11 @@
     "frame_config": {"ref": "hardware"},
 }
 
-galvo_device_types = {"Analog Device": ("NI", "ni"), "ASI Device": ("ASI", "asi"), "Virtual Device": ("Synthetic", "synthetic")}
+galvo_device_types = {
+    "Analog Device": ("NI", "ni"),
+    "ASI Device": ("ASI", "asi"),
+    "Virtual Device": ("Synthetic", "synthetic"),
+}
 
 waveform_types = {
     "Sine": "sine",
@@ -527,7 +534,10 @@
     ],
 }
 
-zoom_device_types = {"Dynamixel": ("Dynamixel", "dynamixel"), "Virtual Device": ("Synthetic", "synthetic")}
+zoom_device_types = {
+    "Dynamixel": ("Dynamixel", "dynamixel"),
+    "Virtual Device": ("Synthetic", "synthetic"),
+}
 
 zoom_position_widgets = {
     "zoom_value": ["Zoom Value", "Input", "string", None, "Example: 16x"],
@@ -576,7 +586,11 @@
     "n_modes": ["Number of Modes", "Input", "int", None, "Example: 32", 32],
 }
 
-laser_device_types = {"Analog Device": ("NI", "ni"), "ASI Laser": ("ASI", "asi"), "Virtual Device": ("Synthetic", "synthetic")}
+laser_device_types = {
+    "Analog Device": ("NI", "ni"),
+    "ASI Laser": ("ASI", "asi"),
+    "Virtual Device": ("Synthetic", "synthetic"),
+}
 
 laser_hardware_widgets = {
     "wavelength": ["Wavelength", "Input", "int", None, "Example: 488", 488],
@@ -676,4 +690,4 @@
     "ASIMFC2000": "MFC2000",
     "GalvoNIStage": "NI",
     "Thorlabs": "KIM001",
-}
+}