Prerequisites

• Install PVCAM drivers, https://downloads.curibio.com/software/nautilus/PVCam_3.9.10.5-PMQI_Release_Setup.zip
• Install NiDAQmx drivers, https://downloads.curibio.com/software/nautilus/ni-daqmx_22.8_online.exe
• Install nautilai software, downloads.curibio.com/software/nautilai/Nautilai-0.1.1-win64.exe

The Nautilai installer by default will install the application and create a start menu shortcut. To start the application find in start menu.

Configuration

On first run the application will create a new config file at C:\Users\<your user>\AppData\Local\Nautilai\nautilai.toml that contains the following settings.

[nautilai]
prefix = "default_"
auto_contrast_brightness = true
outdir = "E:\\"

[device.nidaqmx]
device = "Dev2"
device_2 = "DevOR"
max_voltage = 1.4

[device.photometrics]
trigger_mode = 0
exposure_mode = 5
speed_table_index = 0

[acquisition]
fps = 10.0
duration = 1.0
led_intensity = 50.0
storage_type = 1
auto_tile = true
rows = 2
cols = 3

[acquisition.region]
s1 = 800
p1 = 1000
s2 = 2399
p2 = 2199
sbin = 2
pbin = 2

[acquisition.live_view]
vflip = false
hflip = true

[device.kinetix.line_read_times]
dynamic_range = 3.75
speed = 0.625
sensitivity = 3.53125
sub_electron = 60.1

[device.tango]
com = "COM3"

[nautilai] settings
prefix is the value used as a prefix for each saved image. For example, the final image name using the default value will be as follows default_N_XXX.tiff
where N is a 1-based index of the stage position and XXX is the frame number

auto_contrast_brightness Controls if auto contrast/brightness is applied to the live view image. This does not affect the image that is saved to disk.

[device.nidaqmx] settings

device The name of the nidaqmx device used to control the LED panel. You must create a new device with the National Instruments software and set this value in order for the LED controller to work.

max_voltage The max voltage allowed for the analog output channel.

[device.photometrics] settings
trigger_mode The camera trigger mode is an enum value for the following modes.

0: EXT_TRIG_INTERNAL
1: EXT_TRIG_TRIG_FIRST
2: EXT_TRIG_EDGE_RISING
3: EXT_TRIG_LEVEL
4: EXT_TRIG_SOFTWARE_FIRST
5: EXT_TRIG_SOFTWARE_EDGE
6: EXT_TRIG_LEVEL_OVERLAP
7: EXT_TRIG_LEVEL_PULSED

Refer to the PVCAM documentation for an explanation of each mode.

exposure_mode The camera exposure mode is an enum value for the following modes.

0: EXPOSE_OUT_FIRST_ROW
1: EXPOSE_OUT_ALL_ROWS
2: EXPOSE_OUT_ANY_ROW
3: EXPOSE_OUT_ROLLING_SHUTTER
4: EXPOSE_OUT_LINE_TRIGGER
5: EXPOSE_OUT_GLOBAL_SHUTTER
6: MAX_EXPOSE_OUT_MODE

Refer to the PVCAM documentation for an explanation of each mode.

speed_table_index The index of the camera speed table to use. This value is dependent on the camera. The speed table is logged as output when running the application, if you need to change this value refer to the output and select one of the speed table entries and restart.

[device.tango] settings
com The COM port for the connected stage.

[acquisition] settings
These are the default acquisition settings, all these values can be changed from the application itself, changing the values in the application does not change the default values in the config file.

[acquisition.region] settings
This is the default region to capture, there is no interface in the UI to change these values.

s1 Serial register 1 value.
p1 Parallel register 1 value.
s2 Serial register 2 value.
p2 Parallel register 2 value.
sbin Serial binning factor.
pbin Parallel binning factor.

Depending on the camera sensor the point (s1,p1) will either be the top left corner or the top right corner of the region. The point (s2, p2) will be the bottom right or bottom left respectfully. For more information about the coordinate model refer to the PVCAM documentation.

Running

When running the software you must add at least one stage location through the stage navigation modal, if there are no saved locations the software will not capture any images.

Live view can be on during acquisition, if you start live view and then start an acquisition the live view will remain on after the acquisition is finished. You must stop live view in order to turn off the LED panel.

Log files are stored under C:\Users\<user>\AppData\Nautilai