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Consistency in documentation.
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docs/source/02_user_guide/01_supported_hardware/camera.rst

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@@ -149,9 +149,7 @@ Photometrics
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.. note::
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**navigate** has been tested with the following versions of the Photometric's
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drivers:
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**navigate** has been tested with the following versions of the Photometric's drivers:
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- PVCAM: 3.9.13
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-----------------
@@ -175,6 +173,32 @@ Iris 15
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settle_down: 0.1 #ms
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flip_x: False
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flip_y: False
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|
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-----------------
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Ximea
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--------------------------------
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MU196MR-ON
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~~~~~~~~~~~~~~~~~~~~~~~~~~~
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.. collapse:: Configuration File
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.. code-block:: yaml
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microscopes:
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microscope_name:
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camera:
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hardware:
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type: ximea
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serial_number: 111
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camera_connection: PMPCIECam00
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defect_correct_mode: 2.0
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delay: 1.0 #ms
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settle_down: 0.1 #ms
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flip_x: False
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flip_y: False
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|

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

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@@ -15,8 +15,8 @@ frames, and some jitter in timing is anticipated.
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.. _hardware_ni:
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National Instruments (NI)
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-------------------------
18+
National Instruments
19+
--------------------
2020
In principle, most NI-based data acquisition cards should work with the software, so long
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as there are a sufficient number of analog and digital ports, and the sampling rate (typically 100 kHz)
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is high enough per port.

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

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@@ -53,21 +53,16 @@ file as follows:
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5454
-----------
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Sutter Instruments
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------------------
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ASI
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---
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59-
Lambda 10-3 & 10-B
60-
~~~~~~~~~~~~~~~~~~
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FW-1000
60+
~~~~~~~
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We typically communicate with Sutter Lambda 10-3 controllers via serial port. It is
63-
recommended that you first establish communication with the device using manufacturer
64-
provided software. Alternatively, one can use MicroManager. For some filter wheel types,
65-
the filter_wheel_delay is calculated according to the size of the move and model of the
66-
filter wheel. For other filter wheel types, the filter_wheel_delay is a fixed value, which is specified as
67-
the ``filter_wheel_delay`` entry in the configuration file. The number of filter wheels
68-
connected to the controller is specified as ``wheel_number`` in the configuration file.
69-
Currently, both wheels are moved to the same position, but future implementations will
70-
enable control of both filter wheels independently.
62+
The ASI `filter wheel <https://www.asiimaging
63+
.com/illumination-control/fw-1000-high-speed-filter-wheel/>`_ is controlled by the
64+
ASI Tiger Controller. Thus, you should provide the same ``comport`` entry as you did
65+
for the stage. A single communication instance is used for both the stage and filter wheel.
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.. collapse:: Configuration File
7368

@@ -78,10 +73,10 @@ enable control of both filter wheels independently.
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-
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filter_wheel:
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hardware:
81-
type: SutterFilterWheel
76+
type: ASI
8277
wheel_number: 1
8378
port: COM1
84-
baudrate: 9600
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baudrate: 115200
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filter_wheel_delay: 0.03
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available_filters:
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Empty-Alignment: 0
@@ -91,18 +86,23 @@ enable control of both filter wheels independently.
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9287
|
9388
94-
-------------
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--------------
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96-
ASI
97-
---
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Sutter Instruments
92+
------------------
9893

99-
FW-1000
100-
~~~~~~~
94+
Lambda 10-3 & 10-B
95+
~~~~~~~~~~~~~~~~~~
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102-
The ASI `filter wheel <https://www.asiimaging
103-
.com/illumination-control/fw-1000-high-speed-filter-wheel/>`_ is controlled by the
104-
ASI Tiger Controller. Thus, you should provide the same ``comport`` entry as you did
105-
for the stage. A single communication instance is used for both the stage and filter wheel.
97+
We typically communicate with Sutter Lambda 10-3 controllers via serial port. It is
98+
recommended that you first establish communication with the device using manufacturer
99+
provided software. Alternatively, one can use MicroManager. For some filter wheel types,
100+
the filter_wheel_delay is calculated according to the size of the move and model of the
101+
filter wheel. For other filter wheel types, the filter_wheel_delay is a fixed value, which is specified as
102+
the ``filter_wheel_delay`` entry in the configuration file. The number of filter wheels
103+
connected to the controller is specified as ``wheel_number`` in the configuration file.
104+
Currently, both wheels are moved to the same position, but future implementations will
105+
enable control of both filter wheels independently.
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.. collapse:: Configuration File
108108

@@ -113,10 +113,10 @@ for the stage. A single communication instance is used for both the stage and fi
113113
-
114114
filter_wheel:
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hardware:
116-
type: ASI
116+
type: SutterFilterWheel
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wheel_number: 1
118118
port: COM1
119-
baudrate: 115200
119+
baudrate: 9600
120120
filter_wheel_delay: 0.03
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available_filters:
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Empty-Alignment: 0
@@ -126,7 +126,7 @@ for the stage. A single communication instance is used for both the stage and fi
126126
127127
|
128128
129-
--------------
129+
-------------
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131131
LUDL Electronic Products
132132
------------------------
@@ -164,13 +164,10 @@ MAC6000
164164
165165
-------------
166166

167-
Analog/Digital Devices
168-
----------------------
167+
National Instruments
168+
--------------------
169169

170-
Some manufacturers provide filter wheels that are controlled by analog or digital signals.
171-
Here, each digital signal corresponds to a filter position. The user must specify the
172-
number of filters in the filter wheel and the digital signal that corresponds to each
173-
filter position.
170+
Some manufacturers provide filter wheels that are controlled by analog or digital signals. Here, each digital signal corresponds to a filter position. The user must specify the number of filters in the filter wheel and the digital signal that corresponds to each filter position.
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.. collapse:: Configuration File
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docs/source/02_user_guide/01_supported_hardware/galvo.rst

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@@ -7,13 +7,10 @@ Galvo mirrors are used for fast scanning, shadow reduction, and occasionally as
77

88
------------
99

10-
Analog-Controlled Galvo
11-
-----------------------
10+
National Instruments
11+
--------------------
1212

13-
Multiple types of galvanometers have been used, including Cambridge
14-
Technologies/Novanta, Thorlabs, and ScannerMAX. Each of these devices
15-
are externally controlled via analog signals delivered from a data
16-
acquisition card.
13+
Multiple types of galvanometers have been used, including Cambridge Technologies/Novanta, Thorlabs, and ScannerMAX. Each of these devices are externally controlled via analog signals delivered from an NI-based data acquisition card.
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.. collapse:: Configuration File
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11
======
22
Lasers
33
======
4-
We currently support laser control via voltage signals. In the near-future, we will consider implementing
5-
laser control via serial communication for power control, but digital modulation will still be controlled via
6-
voltage signals.
4+
We currently support laser control via voltage signals. In the near-future, we will consider implementing laser control via serial communication for power control, but digital modulation will still be controlled via voltage signals. The ``onoff`` entry is for digital modulation. The ``power`` entry is for analog modulation.
75

86
---------------------
97

10-
Analog/Digital-Controlled Lasers
11-
--------------------------------
12-
13-
Most lasers are controlled externally via mixed analog and digital modulation.
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The ``onoff`` entry is for digital modulation. The ``power`` entry is for analog
15-
modulation.
8+
Applied Scientific Instrumentation
9+
----------------------------------
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17-
.. note::
18-
Omicron LightHUB Ultra laser launches include both Coherent- and LuxX lasers,
19-
which vary according to wavelength. LuxX lasers should be operated in an ACC
20-
operating mode with the analog modulation option enabled. The Coherent Obis lasers
21-
should be set in the mixed modulation mode.
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23-
.. note::
24-
Coherent Obis lasers should be set in the mixed modulation mode. It is not uncommon
25-
for the slew rate from the data acquisition card to be insufficient to drive the modulation
26-
of the laser if the laser is set to an analog modulation mode.
12+
Tiger Controller
13+
~~~~~~~~~~~~~~~~~~
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28-
.. note::
29-
Users have reported intermittent connection issues at random intervals arising
30-
from USB-based communication instance with Coherent Obis controllers. Specifically,
31-
these errors were observed as a conflict over COM port assignments between the
32-
Coherent OBIS laser and the ASI Tiger controller. These issues are discussed in
33-
depth in the :ref:`communication challenges <obis_tiger_connection>` section.
15+
The Tiger Controller from ASI can also be used to perform analog, digital, and mixed modulation of lasers. Digital modulation is controlled with a `TGPLC <https://asiimaging.com/docs/tiger_programmable_logic_card>`_ or `TGGALVO <https://asiimaging.com/docs/tggalvo>`_ control cards, while analog modulation is controlled with a TGGALVO control card.
3416

17+
--------------------------------
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3619
.. collapse:: Configuration File
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@@ -44,36 +27,48 @@ modulation.
4427
wavelength: 488
4528
onoff:
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hardware:
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type: NI
48-
channel: PXI6733/port0/line2
30+
type: ASI
31+
axis: [2-8]
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min: 0.0
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max: 5.0
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power:
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hardware:
53-
type: NI
54-
channel: PXI6733/ao0
36+
type: ASI
37+
axis: A
5538
min: 0.0
5639
max: 5.0
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-
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wavelength: 561
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onoff:
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hardware:
61-
type: NI
62-
channel: PXI6733/port0/line3
44+
type: ASI
45+
axis: [2-8]
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min: 0.0
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power:
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hardware:
67-
type: NI
68-
channel: PXI6733/ao1
50+
type: ASI
51+
axis: B
6952
min: 0.0
7053
max: 5.0
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55+
7256
-------------------
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75-
Synthetic Lasers
76-
--------------------------------
59+
National Instruments
60+
--------------------
61+
62+
Most lasers are controlled externally via mixed analog and digital modulation. Thus, a NI data acquisition card may be used to control the laser. In general, an analog output can be used to control both the digital and analog modulation of the laser, whereas a digital output can only be used to control the digital modulation of the laser.
63+
64+
.. note::
65+
Omicron LightHUB Ultra laser launches include both Coherent- and LuxX lasers, which vary according to wavelength. LuxX lasers should be operated in an ACC operating mode with the analog modulation option enabled. The Coherent Obis lasers should be set in the mixed modulation mode.
66+
67+
.. note::
68+
Coherent Obis lasers should be set in the mixed modulation mode. It is not uncommon for the slew rate from the data acquisition card to be insufficient to drive the modulation of the laser if the laser is set to an analog modulation mode.
69+
70+
.. note::
71+
Users have reported intermittent connection issues at random intervals arising from USB-based communication instance with Coherent Obis controllers. Specifically, these errors were observed as a conflict over COM port assignments between the Coherent OBIS laser and the ASI Tiger controller. These issues are discussed in depth in the :ref:`communication challenges <obis_tiger_connection>` section.
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.. collapse:: Configuration File
@@ -87,40 +82,38 @@ Synthetic Lasers
8782
wavelength: 488
8883
onoff:
8984
hardware:
90-
type: synthetic
85+
type: NI
9186
channel: PXI6733/port0/line2
9287
min: 0.0
9388
max: 5.0
9489
power:
9590
hardware:
96-
type: synthetic
91+
type: NI
9792
channel: PXI6733/ao0
9893
min: 0.0
9994
max: 5.0
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-
10196
wavelength: 561
10297
onoff:
10398
hardware:
104-
type: synthetic
99+
type: NI
105100
channel: PXI6733/port0/line3
106101
min: 0.0
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max: 5.0
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power:
109104
hardware:
110-
type: synthetic
105+
type: NI
111106
channel: PXI6733/ao1
112107
min: 0.0
113108
max: 5.0
109+
|
114110
115111
-------------------
116112

117-
ASI Laser
118-
119-
We currently support laser control via voltage signals. ASI Tiger Controller-based lasers
120-
are now supported for both digital and analog modulation through the ASILaser class.
121-
Future versions may expand a non-serial-based laser control using the ASI system.
113+
Synthetic Lasers
122114
--------------------------------
123115

116+
124117
.. collapse:: Configuration File
125118

126119
.. code-block:: yaml
@@ -132,29 +125,28 @@ Future versions may expand a non-serial-based laser control using the ASI system
132125
wavelength: 488
133126
onoff:
134127
hardware:
135-
type: ASI
136-
axis: [2-8]
128+
type: synthetic
129+
channel: PXI6733/port0/line2
137130
min: 0.0
138131
max: 5.0
139132
power:
140133
hardware:
141-
type: ASI
142-
axis: A
134+
type: synthetic
135+
channel: PXI6733/ao0
143136
min: 0.0
144137
max: 5.0
145138
-
146139
wavelength: 561
147140
onoff:
148141
hardware:
149-
type: ASI
150-
axis: [2-8]
142+
type: synthetic
143+
channel: PXI6733/port0/line3
151144
min: 0.0
152145
max: 5.0
153146
power:
154147
hardware:
155-
type: ASI
156-
axis: B
148+
type: synthetic
149+
channel: PXI6733/ao1
157150
min: 0.0
158151
max: 5.0
159-
160-
-------------------
152+
|

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

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5858
-------------
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60-
Analog Controlled Voice Coils and Tunable Lenses
61-
------------------------------------------------
60+
National Instruments
61+
--------------------
6262

63-
In principle, this hardware type can support any analog-controlled voice coil or tunable lens.
64-
The `BLINK <https://www.thorlabs.com/thorproduct.cfm?partnumber=BLINK>`_ and the
65-
`Optotune Focus Tunable Lens <https://www.optotune.com/tunable-lenses>`_ are
66-
controlled with an analog signal from the DAQ.
63+
In principle, this hardware type can support any analog-controlled voice coil or tunable lens. The `BLINK <https://www.thorlabs.com/thorproduct.cfm?partnumber=BLINK>`_ and the `Optotune Focus Tunable Lens <https://www.optotune.com/tunable-lenses>`_ are controlled with an analog signal from the DAQ.
6764

6865
-----------------
6966

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