Merge branch 'develop' into 2024-07-13

Author: annie-xd-wang

docs/source/user_guide/case_studies/acquire_exASLM.rst

@@ -12,9 +12,11 @@ To achieve this, **navigate** receives a `trigger signal <http://www.asiimaging.
 from the stage controller to start image acquisition once
 the stage has reached the desired position and velocity. Thereafter, **navigate** acquires images
 at a constant rate until the stage has reached the end position. This mode of acquisition is termed
-"Constant Velocity Acquisition", and is implemented as a feature in **navigate**.
+"Constant Velocity Acquisition", and is implemented as a plugin in **navigate**. To
+download the plugin, please visit `navigate-constant-velocity-acquisition
+<https://github.com/TheDeanLab/navigate-constant-velocity-acquisition>`_.
 
-Furthermore, since the stage moves at a 45 degree angle relative to the microscope detection axis,
+Since the stage moves at a 45 degree angle relative to the microscope detection axis,
 computational shearing of the data is necessary. For large data sets, this can become computationally challenging and
 unnecessarily results in greater data overhead owing to empty space introduced in the data.
 To avoid this, we also provide a guide on how to perform two axis stage

docs/source/user_guide/hardware/dichroic.rst

@@ -0,0 +1,66 @@
+================
+Dichroic Turrets
+================
+
+Dichroics can be used to reflect the excitation light towards the camera, while
+permitting the emission light that is captured by the objective to be transmitted
+to the camera. Alternatively, they can be placed in the detection path to separate
+different emission wavelengths and to direct it to the appropriate camera.
+
+Currently, **navigate** incorporates a dichroic turret as a filter wheel, which enables
+you to add as many different dichroic turrets as you would like.
+
+.. note::
+
+    The `name` parameter under `hardware` is optional. If not provided, the name of the
+    device will be default to Filter 0, Filter 1, ... Filter N in the GUI. However, if
+    is is provided, then the GUI will automatically use the name provided as a label.
+
+ASI
+---
+
+C60-CUBE-SLDR
+~~~~~~~~~~~~~
+
+The `C60-CUBE-SLDR <https://www.asiimaging.com/illumination-control/c60-cube-sldr/>`_
+is a motorized dichroic slider that can be controlled by the ASI Tiger Controller.
+The example below shows the configuration file with one dichroic turret, and one
+filter wheel. The same communication instance is used for both the stage and filter
+wheel. It holds a maximum of 4 dichroics.
+
+
+.. collapse:: Configuration File
+
+    .. code-block:: yaml
+
+      microscopes:
+        microscope_name:
+          -
+            filter_wheel:
+              hardware:
+                type: ASI
+                name: Filter Wheel 1
+                wheel_number: 1
+                port: COM1
+                baudrate: 115200
+              filter_wheel_delay: 0.03
+              available_filters:
+                Empty-Alignment: 0
+                GFP: 1
+                RFP: 2
+                Far-Red: 3
+          -
+            filter_wheel:
+              hardware:
+                type: ASICubeSlider
+                name: Dichroic Turret 1
+                wheel_number: 2
+                port: COM1
+                baudrate: 115200
+              filter_wheel_delay: 0.25
+              available_filters:
+                510LP: 0
+                560LP: 1
+                600LP: 2
+                660LP: 3
+|

docs/source/user_guide/hardware/filter_wheel.rst

@@ -17,6 +17,7 @@ file as follows:
           -
             filter_wheel:
               hardware:
+                name: Lower Filter Wheel
                 type: SutterFilterWheel
                 wheel_number: 1
                 port: COM1
@@ -30,6 +31,7 @@ file as follows:
           -
             filter_wheel:
               hardware:
+                name: Upper Filter Wheel
                 type: SutterFilterWheel
                 wheel_number: 2
                 port: COM1
@@ -42,6 +44,12 @@ file as follows:
                 Far-Red: 3
 |
 
+.. note::
+
+    The `name` parameter under `hardware` is optional. If not provided, the name of the
+    device will be default to Filter 0, Filter 1, ... Filter N in the GUI. However, if
+    is is provided, then the GUI will automatically use the name provided as a label.
+
 -----------
 
 Sutter Instruments
@@ -107,7 +115,7 @@ for the stage. A single communication instance is used for both the stage and fi
                 type: ASI
                 wheel_number: 1
                 port: COM1
-                baudrate: 9600
+                baudrate: 115200
               filter_wheel_delay: 0.03
               available_filters:
                 Empty-Alignment: 0

docs/source/user_guide/hardware/hardware_home.rst

@@ -21,6 +21,7 @@ Additional devices are available by installing the
    remote_focus.rst
    stage.rst
    filter_wheel.rst
+   dichroic.rst
    galvo.rst
    laser.rst
    shutter.rst

docs/source/user_guide/hardware/stage.rst

@@ -72,7 +72,7 @@ first establish communication with the device using `ASI provided software <http
                   stages:
                   refmode:
                   port: COM12
-                  baudrate: 9600
+                  baudrate: 115200
                   timeout: 0.25
               joystick_axes: [x, y, z]
               x_min: -10000.0
@@ -233,7 +233,7 @@ the software is restarted, it should work.
                   serial_number: 001
                   axes: [x, y, z]
                   axes_mapping: [x, y, z]
-                  feedback_alignment: 
+                  feedback_alignment:
                   volts_per_micron: 0.0
                   min: 0.0
                   max: 25000
@@ -314,16 +314,16 @@ C-884
                   serial_number: 119060508
                   axes: [x, y, z, theta, f]
                   axes_mapping: [1, 2, 3, 4, 5]
-                  feedback_alignment: 
+                  feedback_alignment:
                   volts_per_micron: 0.0
-                  min: 
-                  max: 
+                  min:
+                  max:
                   controllername: C-884
                   stages: L-509.20DG10 L-509.40DG10 L-509.20DG10 M-060.DG M-406.4PD NOSTAGE
                   refmode: FRF FRF FRF FRF FRF FRF
-                  port: 
-                  baudrate: 
-                  timeout: 
+                  port:
+                  baudrate:
+                  timeout:
               joystick_axes: [x, y, z]
               x_min: -10000.0
               x_max: 10000.0
@@ -365,16 +365,16 @@ E-709
                   serial_number: 119060508
                   axes: [x, y, z, theta, f]
                   axes_mapping: [1, 2, 3, 4, 5]
-                  feedback_alignment: 
+                  feedback_alignment:
                   volts_per_micron: 0.0
-                  min: 
-                  max: 
+                  min:
+                  max:
                   controllername: E-709
                   stages: L-509.20DG10 L-509.40DG10 L-509.20DG10 M-060.DG M-406.4PD NOSTAGE
                   refmode: FRF FRF FRF FRF FRF FRF
-                  port: 
-                  baudrate: 
-                  timeout: 
+                  port:
+                  baudrate:
+                  timeout:
               joystick_axes: [x, y, z]
               x_min: -10000.0
               x_max: 10000.0
@@ -424,16 +424,16 @@ positioning.
                   serial_number: 74000375
                   axes: [f]
                   axes_mapping: [1]
-                  feedback_alignment: 
+                  feedback_alignment:
                   volts_per_micron: 0.0
-                  min: 
-                  max: 
+                  min:
+                  max:
                   controllername:
-                  stages: 
-                  refmode: 
-                  port: 
-                  baudrate: 
-                  timeout: 
+                  stages:
+                  refmode:
+                  port:
+                  baudrate:
+                  timeout:
               joystick_axes: [f]
               x_min: -10000.0
               x_max: 10000.0
@@ -481,11 +481,11 @@ KST101
                   min: 0
                   max: 25
                   controllername:
-                  stages: 
-                  refmode: 
-                  port: 
-                  baudrate: 
-                  timeout: 
+                  stages:
+                  refmode:
+                  port:
+                  baudrate:
+                  timeout:
               joystick_axes: [f]
               x_min: -10000.0
               x_max: 10000.0

src/navigate/config/config.py

@@ -342,6 +342,7 @@ def verify_experiment_config(manager, configuration):
         "celltype": "MV3",
         "label": "GFP",
         "file_type": "TIFF",
+        "prefix": "Cell_",
         "date": time.strftime("%Y-%m-%d"),
         "solvent": "BABB",
     }
@@ -519,11 +520,6 @@ def verify_experiment_config(manager, configuration):
         "end_focus": 0.0,
         "abs_z_start": 0.0,
         "abs_z_end": 100.0,
-        "scanrange": 500.0,
-        "n_plane": 1.0,
-        "offset_start": 0.0,
-        "offset_end": 9.8,
-        "conpro_cycling_mode": "per_stack",
         "waveform_template": "Default",
     }
     if (

src/navigate/config/configuration_database.py

@@ -57,7 +57,8 @@
 
 filter_wheel_device_types = {
     "Sutter Instruments": "SutterFilterWheel",
-    "Applied Scientific Instrumentation": "ASI",
+    "ASI Filter Wheel": "ASI",
+    "ASI Dichroic Slider": "ASICubeSlider",
     "Ludl Electronic Products": "LUDLFilterWheel",
     "Analog/Digital Device": "NI",
     "Virtual Device": "synthetic",
@@ -85,6 +86,7 @@
     "hardware/wheel_number": ["Number of Wheels", "Spinbox", "int", None, "Example: 1"],
     "hardware/port": ["Serial Port", "Input", "string", None, "Example: COM1"],
     "hardware/baudrate": ["Baudrate", "Input", "int", None, "Example: 9600"],
+    "hardware/name": ["GUI Label", "Input", "string", None, "Example: Filter Wheel 1"],
     "filter_wheel_delay": [
         "Filter Wheel Delay (s)",
         "Input",

src/navigate/config/experiment.yml

@@ -63,11 +63,6 @@ MicroscopeState:
   end_focus: 0.0
   abs_z_start: 0.0
   abs_z_end: 200.0
-  scanrange: 500.0
-  n_plane: 1
-  offset_start: 0.0
-  offset_end: 10.0
-  conpro_cycling_mode: Per Stack
   waveform_template: Default
 MultiPositions:
   [[15000.0,12000.0,15500.0,0.0,70000.0], [35000.0,42000.0,15500.0,0.0,70000.0]]

src/navigate/controller/configuration_controller.py

@@ -396,6 +396,24 @@ def number_of_filter_wheels(self):
             return len(self.microscope_config["filter_wheel"])
         return 1
 
+    @property
+    def filter_wheel_names(self):
+        """Return a list of filter wheel names
+
+        Returns
+        -------
+        filter_wheel_names : list
+            List of filter wheel names.
+        """
+        filter_wheel_names = []
+        if self.microscope_config is not None:
+            for i in range(self.number_of_filter_wheels):
+                name = self.microscope_config["filter_wheel"][i]["hardware"].get(
+                    "name", f"Filter Wheel {i}"
+                )
+                filter_wheel_names.append(name)
+        return filter_wheel_names
+
     @property
     def microscope_list(self):
         """Return a list of microscope names