SciScan is a modular software package and provides different software options depending on the hardware configuration of your microscope. Which hardware is controlled by software can easily be changed by adding or removing software modules from the start-up list in the .ini file.
Module Types
Modules are categorized into 6 different types to help avoid hardware conflicts and make setup easier.
| Name | Suffix | Description |
|---|---|---|
| Common Required | *_crMD.vi | Modules that are required by both the Galvo and Resonant versions of SciScan. |
| Common Optional | *_coMD.vi | Optional modules that can be used with both resonant and galvo based systems. |
| Resonant Required | *_rrMD.vi | Modules that are required by SciScan for resonant scanning systems. |
| Resonant Optional | *_roMD.vi | Optional modules that can only be used with resonant scanning hardware |
| Galvo Optional | *_goMD.vi | Optional modules that can only be used with galvo hardware. |
| Galvo Required | *_grMD.vi | Modules that are required by the galvo version of SciScan to run properly. |
Common Required
Common required modules are modules that are essential for SciScan to run for both the resonant and galvo versions. Both versions use the same software module.
| Name | Type | Function |
|---|---|---|
| z.stack.configure_crMD.vi | Interpreter | Interprets settings specified for z-stack acquisition into appropriate I/O commands for Z-Stage, Intensity change and acquisition timing. |
| fp button handler_crMD.vi | Button Handler | Registers all the reference numbers for GUI controls with the GFG. Also controls simple button interactions. |
Common Optional
The Common Optional Modules, suffixed by *_coMD.vi, are not required for SciScan to function but are required to control various pieces of hardware including; PMT gain, Motorised Intensity Controllers and Pockels cells. Common Optional modules can be used by either galvo scanning hardware or resonant scanning hardware.
| Module Name | Type | Function | Required Hardware |
|---|---|---|---|
| MIC communication_coMD.vi | Hardware driver | Provides USB based serial communication with motorised intensity controller (MIC) | Scientifica Motorised Intensity Control Module |
| MIC_coMD.vi | Front panel handler | Interprets GUI laser power adjustments and passes the value to MIC communication_coMD.vi | N/A |
| motorisedmirrors_coMD.vi | Hardware driver | Controls movement of Scientifica motorised mirrors. | Scientifica Motorised Mirror Module |
| PMT communication_coMD.vi | Hardware driver | Communicates to USB based PMT controller to regulate PMT gain. | Scientifica MDU-8000-10 PMT Controller |
| shutter vi_coMD.vi | DAQ control | Controls the TTL signal to open and close the table shutter. | TTL Triggerable Shutter controller |
| XYZ stage handler_coMD.vi | Front panel handler | Interprets button presses for stage control area passes values to XYZ stage communication_coMD.vi | N/A |
| XYZ stage communication_coMD.vi | Hardware driver | Provides USB based serial communication with XYZ stage controller. | Scientifica SliceScope/Motorised XY Stages |
| PositionSave_coMD.vi | Plugin | Adds Position Save Module plugin to SciScan. | N/A |
| SciScript_coMD.vi | Plugin | Adds macro building (SciScript) functionality to SciScan. | N/A |
| startdelayLUT_coMD.vi | Plugin | Creates a look-up-table to save the most recently used start delay setting for a given set of scan parameters. | N/A |
| OME_coMD.vi | Plugin | Allows users to save images with OME compliant metadata | N/A |
Resonant Required
The Resonant Required Modules are modules which are essential for SciScan’s basic functionality, the software will not work properly without them. Resonant Required modules are only to be used with resonant scanning hardware.
| Module Name | Type | Function |
|---|---|---|
| resonant.calculation vi_rrMD.vi | Calculation | Makes all behind-the-scenes calculations for the resonant scan engine. |
| resonant.display queue to fp display_rrMD.vi | Data Stream | Passes image data from the display queue to the front panel image displays. |
| resonant.image queue to disk and to display queue_rrMD.vi | Data Stream | Passes image data from the image queue to the harddisk for saving as well as to the image queue for eventual display. |
| resonant.raw queue to image queue_rrMD.vi | Data Stream | Passes raw image data from the FPGA FIFO buffer to the image queue. |
| resonant.scan.engine_1.0_rrMD.vi | Scan Engine | Controls I/O for scanning mirrors and image acquisition. |
| resonant.z.stack.run_rrMD.vi | Hardware control and timing. | receives information from z.stack.configure_crMD.vi and coordinates output for scanning, acquisition, motor movement and laser power changes. |
| start_delay_autocorrect_rrMD.vi | Image correction | Automatically tries to find the correct value for the start.delay to correct for bi-directional artefacts using image features. |
Resonant Optional
Resonant Optional modules are modules that are not essential to SciScan’s basic functionality and can only be used with resonant scanning hardware.
| Name | Type | Function | Required Hardware |
|---|---|---|---|
| pockelscontrol_w_blanking_1.0_roMD.vi | Hardware control | Controls output voltage for Pockels cell control. Includes option for turn-around blanking. | Pockels Cell |
Galvo Required
Galvo Required modules are modules that are essential for SciScan to work properly and can only be used with the galvo scanning hardware.
| Name | Type | Function |
|---|---|---|
| calculation vi_grMD.vi | Calculation | Carries out all the behind-the-scenes calculations for the galvo scan engine. |
| display queue to fp display_grMD.vi | Data Stream | Passes image data from the display queue to the front panel displays. |
| galvo.scan.engine_grMD.vi | Scan Engine | Controls I/O tasks for mirror movement and image acquisition based on provided scan waveform. |
| image queue to disk queue_grMD.vi | Data Stream | Passes image data from image queue to hard disk queue for saving. |
| raw queue to image queue_grMD.vi | Data Stream | Passes raw image data from DAQ to the image queue. |
| start_delay_autocorrect_galvo_grMD.vi | Image Correction | Automatically tries to find the correct value for start.delay to correct for bi-directional scanning artefacts. |
| z.stack.run_grMD.vi | Hardware I/O | Coordinates scanning, motor movement, laser power changes for Z-stack acquisition. |
| load_external_cooridnates_grMD.vi | Settings I/O | Allows pixel coordinates in CSV format to be loaded as a line scan trajectory. |
| mark arbitrary waveform_grMD.vi | Calculation | Calculates appropriate waveform for scanner movement during arbitrary line scans based on user-supplied ROI and passes to scan engine |
| standard frame scan geometry_grMD.vi | Calculation | Calculates waveform for standard 2D frame scans based on provided scan parameters before passing it over to the scan engine. |
Galvo Optional
Galvo Optional modules are non-essential modules and typically control peripheral hardware.
| Name | Type | Function | Required Hardware |
|---|---|---|---|
| pockelscontrol_goMD.vi | Hardware control | Creates output task to modulate pockels cell control voltage. | Pockels Cell |