3.b – INI Setup for SciScan 1.3

SciScan includes a small program to help make setting up the .ini file for first use or when upgrading to a new version, called confirmINIsettings.vi. This is located in the INI folder of the LabVIEW Project File.

Please note: confirmINIsettings.vi should only be run from within the SciScan Project. First, launch Sci_Scan.lvproj and run the vi from within the project window, not from windows explorer.

Please note: SciScan’s user interface should not be running while setting up the .ini file.

Please Note: if using LabVIEW 2014, please run the VI GFG 2012 or 2014.vi found in the GFG folder of the SciScan Project to ensure the correct version of the variable engine is used for your version of LabVIEW. confirmINIsettings.vi will appear broken and non-functional until this step has been carried out.

After running confirmINIsettings.vi  (as described below) you shouldn’t need to manually adjust any of the settings in the .ini file to run SciScan but the article below outlines the different settings sections.

Open “confirmINIsettings.vi” by double-clicking on it in the SciScan Project Explorer:

Run “confirmINIsettings.vi” by clicking on the arrow symbol:

Follow the instructions on the user-interface in the correct order step by step:

Start a complete new configuration?

Yes, let’s configure everything from scratch!

Selecting this option, all settings have to be done. Choose this option when this is an installation of a completely new system.

No, I can provide the root path of a previous SciScan installation.

Select this option if you can provide an old installation of SciScan. Simply specify the root path to your old SciScan installation.

Select a DAQ package

In this section you have to select the correct DAQ (data acquisition) package depending on the hardware of your current system. Please refer to the Data acquisition Hardware guide for details of the individual DAQ-Package hardware. There are 6 options in the drop-down menu (left click for selection):

RGG_GG

This is the DAQ package for a full HyperScope system, equipped with two light paths.

The transmitted light path, used for imaging, will be equipped with 1 Resonant mirror (R) and 2 Galvo mirrors (G) = RGG.

The reflected light path, used for photostimulation or imaging, will be equipped with 2 Galvo mirrors (G) = _GG.

RG_GG

This is the DAQ package for a HyperScope system, equipped with two light paths, but Resonant imaging on the transmitted light path only.

The transmitted light path, used for imaging, will be equipped with 1 Resonant mirror (R) and 1 Galvo mirror (G) = RG.

The reflected light path, used for photostimulation or imaging, will be equipped with 2 Galvo mirrors (G) = _GG.

GG_GG

This is the DAQ package for a HyperScope system, equipped with two light paths, but Galvo imaging and photostimulation only.

The transmitted light path, used for imaging, will be equipped with 2 Galvo mirrors (G) = GG.

The reflected light path, used for photostimulation or imaging, will be equipped with 2 Galvo mirrors (G) = _GG.

RGG

This is the DAQ package for a HyperScope system, equipped with only one light path.

The transmitted light path, used for imaging, will be equipped with 1 Resonant mirror (R) and 2 Galvo mirrors (G) = RGG.

Note, that photostimulation is also available with this option, but without simultaneous imaging possibility.

RG (standalone)

This is the DAQ package for a HyperScope equipped with only one light path, an MP-2050 or an MP-2070 system.

The single light path, used for imaging, will be equipped with 1 Resonant mirror (R) and 1 Galvo mirror (G) = RG.

Note that photostimulation won’t be available with this option.

GG (standalone)

This is the DAQ package for a HyperScope equipped with only one light path (GG), an MP-1000, MP-2000 or 100794 (Galvo for Vivoscope) system.

The single light path, used for imaging, will be equipped with 2 Galvo mirrors (G) = GG.

Note that photostimulation is also available with this option, but without simultaneous imaging possibility.

Specify the detector switch COM port (Linkbone)

Once the correct DAQ package has been selected, this option is either active or greyed out. Obviously, if it is greyed out, ignore this option and continue to the next (GG_GG, RG or GG options).

If this option is active (RGG_GG, RG_GG, RGG only!), please specify the correct COM port of the detector switching device on this system (Linkbone):

Are you unsure what the correct port is? If the Linkbone is properly connected to the workstation (via serial port or USB adapter), it will appear in the windows device manager. As the ports aren’t labelled, you can find out which port is the Linkbone port by disconnecting it from the workstation whilst observing the list of COM ports in the device manager. The disappeared port is the one you are looking for. Don’t forget to reconnect after this check!

Specify the shutter port for the photostimulation light path

Once the correct DAQ package has been selected, this option is either active or greyed out. Obviously, if it is greyed out, ignore this option and continue to the next (RGG, RG or GG DAQ packages).

If this option is active (RGG_GG, RG_GG, GG_GG only!), you can specify the correct port for the shutter of the reflective (photostimulation) light path here. Note that this is only required when the wiring is different to the default wiring. In addition, a warning will be displayed for any attempt to change this setting:

Select optional modules and confirm hardware

This option will be available once all steps have been followed so far. If the selected DAQ package only consists of Galvo mirrors (GG_GG) or this is a standalone option (RG or GG), you have to do this step only once. In all other cases, this configuration must be done for Resonant and Galvo mirrors separately (RGG_GG, RG_GG, RGG). This will also allow you to set up each of them differently if required (e.g. different optional modules loaded for Resonant and Galvo imaging).

Once you click on the “Configure” button, either you will configure a single set of settings or a pop-up message appears, asking with which to start at (order does not matter in this case):

After that, the configuration windows will pop-up:

Configure Resonant hardware

Note that this window only appears for a Resonant scanner!

AO card model options:

  • PXI6259 (for backward compatibility only)
  • PXIe6341 (for all HyperScopes and current revisions of MP-2050 / MP-2070)

digitizer model options:

  • NI5751 (for backward compatibility only)
  • NI5754 (for all HyperScopes and current revisions of MP-2050/ MP-2070)

FPGA model options:

  • PXIe7962R (for backward compatibility only)
  • PXIe7961R (all HyperScopes and current revisions of MP-2050 / MP-2070)

FPGA device name options:

  • usually, this will be “RIO0“, but might deviate depending on the name given in the NI-MAX (Measurement and Automation Explorer). This drop-down menu automatically scans for names – left click on it to see a list of found devices (usually just one per system).

Configure optional modules

Here optional modules can be selected. Just drag and drop the modules to the Active or Inactive side accordingly. A list of all available modules and a description can be found here. Click on “Confirm settings” once you are done.

Configure COM ports and Imaging Shutter

In this menu, the COM ports for the stage control, optional MIC (motorised intensity controller), PMT controller and the optional MM (motorised mirrors) module can be specified. If you are not sure what the correct port of each individual device is, double check with the windows device manager. As the ports aren’t labelled, you can find out which port is the correct port by disconnecting a specific device from the workstation whilst observing the list of COM ports in the device manager. The disappeared port is the one you are looking for. Don’t forget to reconnect after this check!

Also, the IMAGING shutter port is specified there (transmitted light path or the shutter for single light path systems). If the system has default wiring, the given port is already correct.

Once again! (only for RGG_GG, RG_GG or RGG DAQ packages)

Once again click on the “Configure” button. This time, configure the second scanner (either Resonant or Galvo, depending on your first selection). Follow one more time the instructions from 3.5.1) to 3.5.3).

In addition, you can use the same port configurations, selected in the first round:

Done!

If all configurations are done, the following message will appear:

In addition, the green indicators beside the “Configure” button will be active. The indicators that do not apply to the current system will be greyed out.

Quit

If you decide to stop or finish the configuration, you can click on the “Quit” button. Pop-up messages will appear when you did not complete the configuration.

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