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.
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.
axes: [x, y, z, f]
axes_mapping: [M, Y, X, Z]
Applied Scientific Instrumentation
Tiger Controller
The ASI Tiger Controller. is a multi-purpose controller for ASI stages, filter wheels, dichroic sliders, and more. We communicate with Tiger Controllers via a serial port. It is recommended that you first establish communication with the device using ASI provided software.
Note
navigate has been tested with the following versions of the ASI’s Tiger Controller software:
Tiger Controller 2.2.0.
Note
Some users have reported intermittent connection issues at random intervals when used with Coherent OBIS lasers. These issues, and how to address them, are discussed in the communication challenges section.
Warning
If you are using the FTP-2000 stage, do not change the F stage axis. This will differentially drive the two vertical posts, causing them to torque and potentially damage one another.
Tip
ASI stage’s include a configuration option, feedback_alignment, which
corresponds to the Tiger Controller AA Command.
Configuration File
microscopes:
microscope_name:
stage:
hardware:
-
type: ASI
serial_number: 001
axes: [x, y, z, theta, f]
axes_mapping: [A, B, C, D, E]
feedback_alignment: [90, 90, 90, 5, 90]
volts_per_micron: 0.0
min: 0.0
max: 1.0
controllername:
stages:
refmode:
port: COM12
baudrate: 115200
timeout: 0.25
joystick_axes: [x, y, z]
x_min: -10000.0
x_max: 10000.0
y_min: -10000.0
y_max: 10000.0
z_min: -10000.0
z_max: 10000.0
theta_min: 0.0
theta_max: 360.0
f_min: -10000.0
f_max: 10000.0
x_offset: 0.0
y_offset: 0.0
z_offset: 0.0
theta_offset: 0.0
f_offset: 0.0
flip_x: False
flip_y: False
flip_z: False
flip_f: False
MFC2000
Configuration File
microscopes:
microscope_name:
stage:
hardware:
-
type: MFC2000
serial_number: 001
axes: [x, y, z, theta, f]
axes_mapping: [A, B, C, D, E]
feedback_alignment: [90, 90, 90, 5, 90]
volts_per_micron: 0.0
min: 0.0
max: 1.0
controllername:
stages:
refmode:
port: COM12
baudrate: 9600
timeout: 0.25
joystick_axes: [x, y, z]
x_min: -10000.0
x_max: 10000.0
y_min: -10000.0
y_max: 10000.0
z_min: -10000.0
z_max: 10000.0
theta_min: 0.0
theta_max: 360.0
f_min: -10000.0
f_max: 10000.0
x_offset: 0.0
y_offset: 0.0
z_offset: 0.0
theta_offset: 0.0
f_offset: 0.0
flip_x: False
flip_y: False
flip_z: False
flip_f: False
MS2000
Configuration File
microscopes:
microscope_name:
stage:
hardware:
-
type: MS2000
serial_number: 001
axes: [x, y, z, theta, f]
axes_mapping: [A, B, C, D, E]
feedback_alignment: [90, 90, 90, 5, 90]
volts_per_micron: 0.0
min: 0.0
max: 1.0
controllername:
stages:
refmode:
port: COM12
baudrate: 9600
timeout: 0.25
joystick_axes: [x, y, z]
x_min: -10000.0
x_max: 10000.0
y_min: -10000.0
y_max: 10000.0
z_min: -10000.0
z_max: 10000.0
theta_min: 0.0
theta_max: 360.0
f_min: -10000.0
f_max: 10000.0
x_offset: 0.0
y_offset: 0.0
z_offset: 0.0
theta_offset: 0.0
f_offset: 0.0
flip_x: False
flip_y: False
flip_z: False
flip_f: False
Sutter Instruments
MP-285
The Sutter MP-285 communicates via serial port and is quite particular. We have done our best to ensure the communication is stable, but occasionally the stage will send or receive an extra character, throwing off communication. In this case, the MP-285’s screen will be covered in 0s, 1s or look garbled. If this happens, simply turn off the software, power cycle the stage, and press the “MOVE” button on the MP-285 controller once. When the software is restarted, it should work.
Tip
Sometimes the Coherent Connection software messes with the MP-285 serial communication if it is connected to the lasers.
Configuration File
microscopes:
microscope_name:
stage:
hardware:
-
type: MP285
serial_number: 001
axes: [x, y, z]
axes_mapping: [x, y, z]
feedback_alignment:
volts_per_micron: 0.0
min: 0.0
max: 25000
controllername:
stages:
refmode:
port: COM1
baudrate: 9600
timeout: 0.25
joystick_axes: [x, y, z]
x_min: -10000.0
x_max: 10000.0
y_min: -10000.0
y_max: 10000.0
z_min: -10000.0
z_max: 10000.0
theta_min: 0.0
theta_max: 360.0
f_min: -10000.0
f_max: 10000.0
x_offset: 0.0
y_offset: 0.0
z_offset: 0.0
theta_offset: 0.0
f_offset: 0.0
flip_x: False
flip_y: False
flip_z: False
flip_f: False
Physik Instrumente
These stages are controlled by PI’s own Python code and are quite stable.
Note
navigate has been tested with the following versions of the Physik Instrumente software and drivers:
PIMikroMove: 2.36.1.0
PI_GCS2_DLL: 3.22.0.0
They
include a special hardware option, refmode, which corresponds to how the
PI stage chooses to self-reference. Options are REF, FRF, MNL, FNL,
MPL or FPL. These are PI’s GCS commands, and the correct reference mode
for your stage should be found by launching PIMikroMove, which should come with
your stage. Stage names (e.g. L-509.20DG10) can also be found in PIMikroMove
or on a label on the side of your stage.
Note
PI L-509.20DG10 has a unidirectional repeatability of 100 nm, bidirectional repeatability of 2 microns, and a minimum incremental motion of 100 nm. This is potentially too coarse.
C-884
Configuration File
microscopes:
microscope_name:
stage:
hardware:
-
type: PI
serial_number: 119060508
axes: [x, y, z, theta, f]
axes_mapping: [1, 2, 3, 4, 5]
feedback_alignment:
volts_per_micron: 0.0
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:
joystick_axes: [x, y, z]
x_min: -10000.0
x_max: 10000.0
y_min: -10000.0
y_max: 10000.0
z_min: -10000.0
z_max: 10000.0
theta_min: 0.0
theta_max: 360.0
f_min: -10000.0
f_max: 10000.0
x_offset: 0.0
y_offset: 0.0
z_offset: 0.0
theta_offset: 0.0
f_offset: 0.0
flip_x: False
flip_y: False
flip_z: False
flip_f: False
E-709
Configuration File
microscopes:
microscope_name:
stage:
hardware:
-
type: PI
serial_number: 119060508
axes: [x, y, z, theta, f]
axes_mapping: [1, 2, 3, 4, 5]
feedback_alignment:
volts_per_micron: 0.0
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:
joystick_axes: [x, y, z]
x_min: -10000.0
x_max: 10000.0
y_min: -10000.0
y_max: 10000.0
z_min: -10000.0
z_max: 10000.0
theta_min: 0.0
theta_max: 360.0
f_min: -10000.0
f_max: 10000.0
x_offset: 0.0
y_offset: 0.0
z_offset: 0.0
theta_offset: 0.0
f_offset: 0.0
flip_x: False
flip_y: False
flip_z: False
flip_f: False
Thorlabs
KIM001
navigate supports the KIM001 controller. However, this device shows significant hysteresis, and thus we do not recommend it for precise positioning tasks (e.g., autofocusing). It serves as a cost-effective solution for manual, user-driven positioning.
Configuration File
microscopes:
microscope_name:
stage:
hardware:
-
type: Thorlabs
serial_number: 74000375
axes: [f]
axes_mapping: [1]
feedback_alignment:
volts_per_micron: 0.0
min:
max:
controllername:
stages:
refmode:
port:
baudrate:
timeout:
joystick_axes: [f]
x_min: -10000.0
x_max: 10000.0
y_min: -10000.0
y_max: 10000.0
z_min: -10000.0
z_max: 10000.0
theta_min: 0.0
theta_max: 360.0
f_min: -10000.0
f_max: 10000.0
x_offset: 0.0
y_offset: 0.0
z_offset: 0.0
theta_offset: 0.0
f_offset: 0.0
flip_x: False
flip_y: False
flip_z: False
flip_f: False
KST101
Configuration File
microscopes:
microscope_name:
stage:
hardware:
-
type: KST101
serial_number: 26001318
axes: [f]
axes_mapping: [1]
feedback_alignment:
device_units_per_mm: 20000000/9.957067
volts_per_micron: 0.0
min: 0
max: 25
controllername:
stages:
refmode:
port:
baudrate:
timeout:
joystick_axes: [f]
x_min: -10000.0
x_max: 10000.0
y_min: -10000.0
y_max: 10000.0
z_min: -10000.0
z_max: 10000.0
theta_min: 0.0
theta_max: 360.0
f_min: -10000.0
f_max: 10000.0
x_offset: 0.0
y_offset: 0.0
z_offset: 0.0
theta_offset: 0.0
f_offset: 0.0
flip_x: False
flip_y: False
flip_z: False
flip_f: False
Analog-Controlled Galvo/Piezo
We sometimes control position via a galvo or piezo with no software API.
In this case, we treat a standard galvo mirror or piezo as a stage axis. We control the
“stage” via voltages sent to the galvo or piezo. The volts_per_micron setting
allows the user to pass an equation that converts position in microns X, which is
passed from the software stage controls, to a voltage. Note that we use
GalvoNIStage whether or not the device is a galvo or a piezo since the logic is
identical. The voltage signal is delivered via the data acquisition card specified in the
axes_mapping entry.
Note
The parameters distance_threshold and settle_duration_ms are used to provide
a settle time for large moves. if the move is larger than the distance_threshold,
then a wait duration of settle_duration_ms is used to allow the stage to settle
before the image is acquired.
Configuration File
microscopes:
microscope_name:
stage:
hardware:
-
type: GalvoNIStage
serial_number: 001
axes: [Z]
axes_mapping: [PCI6738/ao6]
volts_per_micron: 0.05*x
min: 0.0
max: 1.0
distance_threshold: 5
settle_duration_ms: 5
controllername:
stages:
refmode:
port:
baudrate: 0
joystick_axes: [f]
x_min: -10000.0
x_max: 10000.0
y_min: -10000.0
y_max: 10000.0
z_min: -10000.0
z_max: 10000.0
theta_min: 0.0
theta_max: 360.0
f_min: -10000.0
f_max: 10000.0
x_offset: 0.0
y_offset: 0.0
z_offset: 0.0
theta_offset: 0.0
f_offset: 0.0
flip_x: False
flip_y: False
flip_z: False
flip_f: False
Synthetic Stage
If no stage is present for a particular axis, one must configure the software to use a synthetic stage. For example, not all microscopes have a theta axis.
Configuration File
microscopes:
microscope_name:
stage:
hardware:
-
type: synthetic
serial_number: 001
axes: [x, y, z, theta, f]
axes_mapping: [A, B, C, D, E]
volts_per_micron: 0.0
min: 0.0
max: 1.0
controllername:
stages:
refmode:
port:
baudrate: 0
joystick_axes: [x, y, z]
x_min: -10000.0
x_max: 10000.0
y_min: -10000.0
y_max: 10000.0
z_min: -10000.0
z_max: 10000.0
theta_min: 0.0
theta_max: 360.0
f_min: -10000.0
f_max: 10000.0
x_offset: 0.0
y_offset: 0.0
z_offset: 0.0
theta_offset: 0.0
f_offset: 0.0
flip_x: False
flip_y: False
flip_z: False
flip_f: False