Glossary¶

This page defines the terms that appear in the Configurator interface and in this documentation. Terms are grouped by the stage of work in which they are encountered.

Application and configuration¶

Configurator

The application that produces a configuration for a microscopy system: the hardware in use, how it is wired to the device controller, and the interface offered by the imaging software.

Configuration

The complete description of one system, stored in a folder and opened as a tab in the Configurator. It holds the imported hardware, the selected functions and their startup values, the connections, the Imaging Software layout, and the calibrations.

Hardware Library

The catalog of hardware descriptions supplied by the Device Controller firmware. It is loaded when the Configurator connects to the Device Controller, and it populates the Available Hardware list used to import devices.

Imported devices are listed in the Imported Hardware tree, which is the working area of the hardware stage.

External Resources

Directories added in the application settings that hold driver libraries outside the Inscoper installation, such as Micro-Manager or vendor DLLs. Devices driven through those libraries cannot be configured until the directory is declared.

Expert Mode

The operating mode that exposes the settings required for commissioning and troubleshooting. The default is User Mode, which hides them. A single toggle in the Configurator settings switches between them. See Expert Mode.

Log Level

The verbosity of a log. The Configurator log and the API log are set independently in the application settings. Levels are inclusive: selecting Debug also records Info, Warning, Error, and Fatal messages.

Log Level	Description
All	Records every message.
Trace	Fine-grained information for in-depth debugging.
Debug	Detailed information for diagnosing an issue.
Info	Normal application events.
Warning	An unexpected situation that does not halt the application.
Error	An issue that prevents a specific function from operating.
Fatal	A critical failure in which core functions are lost.
Off	Disables logging.

Distance Unit

The unit (nm, µm, or mm) in which the Configurator displays and accepts every distance value, such as a stage or focus startup value or a piezo range. It is set in Settings > Edit Settings and applies to the whole application, not per field. It changes how a value is shown and typed, not the physical quantity it represents.

Time Unit

The equivalent of distance unit for time values, such as a camera Exposure. It is also set in Settings > Edit Settings, with a choice of ns, µs, ms, or s.

API

The Inscoper API, the software layer through which the Configurator and the imaging software communicate with the device controller. Its version is reported in Help > About.

Hardware¶

Hardware

A peripheral of the system, either physical or virtual (software-defined). Each hardware item is controlled by a driver and is described by a set of parameters. A hardware item connects either to the device controller or directly to the computer, as a USB camera does.

In the Imported Hardware tree, one entry represents one hardware item; its children are its function groups.

Driver

The software component that controls a hardware item. A driver comes either from the device controller, through its hardware library, or from a library installed on the computer, such as Micro-Manager or a vendor DLL, declared as an external resource. At startup, the Configurator reports the number of drivers found per source. Some hardware items, such as a triggered camera, use both kinds of driver.

Group

A set of elements that corresponds to one function of the instrument, such as a turret, a shutter, a focus axis, or a stage axis. Selecting a group in the tree opens its Parameters table. See Configuring a device.

Parameter

An input value of a function, exposed in the parameters table of its group. Each row offers the parameter Name and its startup value. In expert mode, the table also shows the type column.

Startup Value

The value applied to a parameter when the system initializes. Select the checkbox to enable the value, then enter it. When the checkbox is cleared, the device keeps its current state instead of having it overwritten. A startup value is mandatory for the parameters flagged by an orange dot in the tree. See Startup values.

Type

The data type of a parameter, as declared by the firmware: UINT8, INT8, UINT16, INT16, UINT32, INT32, UINT64, INT64, FLOAT, DOUBLE, or STRING. Visible in expert mode only.

Advanced Parameters

The parameters of a camera group that are not exposed in normal operation. Open them with the Advanced Camera Parameters button, available in expert mode only. Not to be confused with the Advanced Parameters window, opened by the gear icon of the Hardware Configuration header, which holds the Calibration and External Parameters tabs.

External Parameters

Instrument-wide Imaging Software settings that belong to no single device: default mosaic overlap, focus map and Jetraw discriminants, USB reset at startup, emulation, white balance, and the device assignments of the FLIM and Sparq modules. See External Parameters.

Setup Wizard

The guided sequence that opens after hardware importation and presents, for each newly imported device, the steps it still requires: device configuration, connection assignment, role assignment for ambiguous elements, and turret configuration. Using it is optional. See Setup wizard.

Scan

The interrogation of the physically connected hardware. The wizard uses it to detect which of the imported devices respond, and to pre-fill their hardware identifiers, such as ports, addresses, and serial numbers. In a device view, Re-Scan repeats the operation and removes the functions the device does not report. A scan requires the Device Controller to be connected.

Turrets and filters¶

Turret: A motorized holder whose positions must be described one by one, so that the imaging software can offer them by name rather than by index. Three types are supported: objective turret, filter cube turret, and filter wheel. A turret group adds a slot table below the standard parameters table. See Turrets and filter wheels.
Slot: One position of a turret. The slot number is the value sent to the hardware; the Display Name is the label shown to the user. Objective slots also carry a Magnification and an NA (numerical aperture), from which the Imaging Software computes the pixel size and the scale bar.
Filter Manager: The window that holds the optics library, the shared list of optical filters and dichroics available to filter cube turrets and filter wheels. Each entry carries its transmittance ranges (and, for a dichroic, its reflectance ranges), expressed as wavelength and transmittance pairs, and is displayed in the light spectrum visualizer. Open it with Settings > Filter Manager.

Camera¶

Camera

A hardware item that acquires image data. A camera manages its own image buffers, acquisition parameters, and triggering modes.

Trigger Option

The source that triggers a camera, selected among the radio buttons of the camera device view. The options list every device that can trigger that camera, such as a co-located Inscoper trigger device or a shared ConfocalNL controller. No Trigger is always offered; select it when no other device triggers the camera, for example a camera connected to the computer by USB only. See Camera trigger.

Camera Stream

The method that triggers image acquisition and controls exposure timing. It determines whether the camera exposes autonomously, on a software command, or on an external hardware signal. The streams derived for each camera are listed, read-only, in the Camera Streams tab of Advanced Camera Parameters, in expert mode.

Stream	Description
Internal	The camera exposes autonomously. Used for Live and snap operations, and for acquisitions that require no hardware driving.
Soft Trig	The camera is triggered by a software command; exposure time is handled by the computer.
Edge Trig	The camera is triggered by an external TTL edge; exposure time is internal to the camera and cannot vary within a sequence.
Level Trig	The camera is triggered by an external TTL level; exposure lasts as long as the level is asserted, which allows different exposure times within one sequence.

Snap

The acquisition of a single image, as opposed to the continuous acquisition started by Start Acq and ended by Stop Acq. The three functions are reported, read-only, in Advanced Camera Parameters.

Note

On some cameras, such as Maico or PcoFlim, one snap acquires several images — different wavelengths for Maico, different phases for PcoFlim.

Shutter¶

Shutter: A motorized element, inside or outside the microscope, that passes or blocks the beam of a light source.

Note

The values used for the two states (0/1, True/False) depend on the implementation of the device.
Open Only When Imaging: A shutter option. When it is enabled, the shutter opens only while the camera is acquiring. At all other times it stays closed to protect the sample, even when the software requests it open.

Device Controller¶

Device Controller

The Inscoper hardware unit (DC) that executes acquisition sequences and manages high-speed synchronization between devices. The Box Type identifies the model, and with it the number of TTL, analog, and serial ports available.

Firmware

The software running inside the Device Controller. It executes the sequences it receives from the imaging software, and it supplies the hardware descriptions and the configuration views used by the Configurator. It is updated with Help > Update Firmware and restarted with Restart Firmware.

Connections

A connection is the physical channel through which a function of a device is controlled. The connection view maps each function that requires wiring to a port of the device controller. See Connections.

Key concepts:

One connection cell is displayed per function that requires wiring; clearing the function in the device view removes its cell.
A cell can only be dropped on a port that carries the signal it needs.
A red outline marks a cell whose link is still missing.
Connection assignment applies to devices driven by the Device Controller. Micro-Manager and custom drivers handle their own communication through their libraries.

Example

A motorized filter wheel might use a Serial connection to send position commands and read status, a TTL Input to read a home position sensor, and a TTL Output to report movement completion.

USB View

The list of USB devices that the device controller currently sees, shown when a connection cell is dropped on the USB port. Each row reports the VID and PID — the Vendor and Product identifiers that distinguish a USB peripheral — together with the manufacturer, product, serial number, driver, hub, and port.

Reset Usb View rescans the USB bus and reloads the table; the delay observed before the table is read back is set by Seconds To Wait After USB Reset in the application settings.

Inscoper Imaging Software¶

Imaging Software: The acquisition software (IIS) that loads the configuration produced by the Configurator. The Configurator defines the interface that the Imaging Software presents: which controls exist, how they are laid out, how each one is rendered, and which calibrations are available.
Control: The element of the Imaging Software interface through which the end user reads or sets one parameter, such as an objective selector, a shutter switch, or an exposure time field. Each control is placed in a category of the layout, and its display type sets the widget used to render it: a drop-down menu, a switch, a slider, or a joystick. See Imaging Software advanced settings.
Layout: The arrangement of the Imaging Software controls, defined in the layout editor of the second stage. The Configurator builds a first layout from the configured hardware; the editor refines it. See Imaging Software layout.
Zone: One of the four destinations of the layout: Settings for instrument-wide values, Channels for values that change from one acquisition channel to the next, Shortcut for controls promoted to the shortcut bar, and Advanced for controls reserved for commissioning.
Category: A named card inside a zone that groups controls. Categories are created, renamed, and removed in the layout editor. They also define the groups of controls that the Imaging Software presents.
Display Type: The kind of widget the Imaging Software uses for a control: SELECT for a fixed set of named states, SWITCHER for a two-state parameter, NUMBER for a numeric parameter, or TEXT for a read-only string. Each type exposes its own settings, such as the value table of a SELECT or the bounds and unit of a NUMBER. See Imaging Software advanced settings.
Conversion Factor: The multiplier applied between the value displayed to the user and the value sent to the hardware, for a NUMBER control.

Calibration¶

Calibration

A model that records a dependency between parameters, so that the Imaging Software can supply the correct value for the current state of the instrument — a correction collar or a stage travel range that depends on the objective in place, for example. See Calibration.

Type	Description
Linear	`sd1 = a * sd2 + b`.
Linear Delta	Variant of the linear formula that exposes the alpha parameter in the Imaging Software (used for soSPIM).
Bilinear	A 3D plane (`ax + by + c`).
Piecewise Linear	Curve approximation by segments.
Constant	A fixed value between two parameters.
Formula	A custom formula, whose free terms are declared in the Variable table.

Discriminant

The parameter whose value selects which calibration entry applies. Each calibration is stored per combination of discriminant values, so changing a discriminant invalidates the current entry. The objective turret is the usual discriminant.

Example

In a FRAP calibration, changing the objective or the filter calls for a new calibration.

Target

The parameter whose value the calibration supplies for each state of the discriminant.

Interpolator

The parameter used by the formula to compute the value of a target — the parameter other than the discriminant. Formulas with two independent variables use Interpolator 1 and Interpolator 2.

Example

In sd1 = a * sd2 + b:

sd1: target.
sd2: interpolator.
a and b: computed during the calibration.

Camera Dependent

Marks a calibration whose recorded values differ from one camera to another.

Auto Update

Marks a calibration that is recomputed automatically when its discriminant changes. The Auto Update Name is the label under which the automatic update is offered to the user.