FAQ

Moving Clarity to a new PC is definitely possible – there are just a few things you’ll need to check:

• Clarity version: Older versions may not run on modern Windows systems. You might need to purchase an upgrade if you're coming from an old version (e.g. Clarity 5.x on Windows XP or Vista). For full details, see our Upgrade Policy.
• Hardware key: RkUSB keys (typically blue) will be problematic on Windows 10 or Windows 11 computers, as their driver requires turning off the "Memory integrity" option in Core Isolation settings. We recommend replacing the RkUSB key with a RkNDUSB (grey, part number S016), which is fully supported on modern systems.
• A/D converter: Some older A/D converters may not work on modern PCs, and we recommend replacing them with a Colibrick, our current A/D converter designed for compatibility with modern systems:
  • U-PAD is only supported on 32-bit operating systems and cannot be used on Windows 11.
  • INT7/INT9 require a PCI slot, which most modern computers no longer have.
• Data and settings: If the old hard drive is still accessible, you can transfer your data and configurations. Detailed steps are available in this FAQ article.

You can also check our Clarity Compatibility page for details about supported Windows versions and hardware requirements.

In such case, it is recommended to check Colibrick Setup in the System Configuration window. Synchronize Start with Digital Input should only be enabled when one of Colibrick's digital inputs is configured as Exr. Start Dig. Input:. Furthermore, Synchronize Start with Digital Input and Exr. Start Dig. Input: must be set to the same Digital Input.
This change was made because the wrong setting led to random issues with analysis starts in previous versions.

Synchronize Start with Digital Input enables a faster and more accurate synchronization of channels with the start signal. The start of the analysis is defined by a marker in data points rather than by detecting the change in Digital Input. The difference is in the order of hundreds of milliseconds, which means that it is important only for very short analysis. When measuring multi-detector chromatograms it will minimize the time shift between detector signals and thus improve the detection of peaks.

We highly recommend registering every license. Only registered users can access our download center and are entitled to obtain a free upgrade to the new version if they are in the one-year free upgrade period. Registration is also a prerequisite to contacting customer support.

Clarity installation requires a specific version of Microsoft .NET Framework, which may not be installed or enabled on the computer by default. You will be notified by the Clarity installer which version of .NET is missing on your PC.

Some external control modules and their components may also require a different version, which is not controlled by the Clarity installer.

There are three ways to obtain the required versions of .NET framework:

• Install the version of .NET supplied in the installation media folder dotNet.
• Download the version of .NET from the internet, using the links below, and install it.
• Turn on Windows updates to download the latest version.

Required versions of .NET Framework

• Clarity installation requires a version of .NET Framework 4.8 or higher
• Installation Qualification for Knauer HPLC requires .NET Framework 3.5 SP1

.NET Framework installation

On Windows 7, download the respective versions using the link below:

Click here to download .NET 3.5 SP1

Click here to download .NET 4.8 (this includes all previous 4.X versions)

On Windows 8.1, 10 and 11 follow these steps:

• Go to Start Menu –> Control Panel –> Programs and Features –> Turn Windows features on or off. (Or in the Run dialog, enter "optionalfeatures".)
• In the displayed Windows Features dialog, check the .NET Framework 3.5 (includes .NET 2.0 and 3.0) and .NET Framework 4.X.

• Click OK, and the selected option will be installed and enabled.

Note:
Installing the .NET framework may require additional Windows updates. Always follow the instructions supplied with each version of .NET you are installing. It contains information about additional updates and security fixes.
Installation of .NET 3.5 is not always smooth in Windows 10, consult with your IT to find the best way to install it.

Serial Number (S/N) and User Code (U/C) are two essential identifiers for our software.

The S/N is a 7- or 8-digit number representing the station's serial number. It is saved in the HW key and is permanent, meaning it doesn't change with the Clarity configuration change. Whenever you ask for technical support at support@dataapex.com, you will have to provide your S/N.

On the other hand, U/C is a 16- or 17-digit code that defines the configuration and version of the chromatography software. It is formed from letters and numbers and unlocks the specific Clarity configuration in a specific HW key. You will need to enter the U/C during the installation process, and when the configuration changes, you must set the new U/C (usually received via email) in the Clarity main window - Help - User Code... dialog.

S/N and U/C can be found on the packing list, and installation media. You can also read the S/N and U/C from within the software (main window – menu Help/About).

If you purchase a software upgrade for your Clarity or Clarity Lite Software license, you will get a free upgrade for your associated free Clarity Offline. You only need to list the Clarity Offline S/N on your purchase order as well. An educational discount also applies to software upgrades.

There may be multiple different reasons. Please check the detailed status in the Instrument window and Device Monitor.

1. Waiting for Injection - indicates parameters for injection were sent to the sampler, but the start signal has not yet been received.
   Suppose the sampler is not working on the injection. In that case, it may indicate wrong synchronization settings in the System Configuration or that the start signal was not received or ignored for some reason.
2. Waiting for Hardware to be Ready to Run - indicates some of the devices configured on the instrument do not report Ready state.
   Check the status reported by individual devices in the Device Monitor.
3. Sequence Paused - indicates the sequence was paused.
   An automatic pause may happen if an invalid value is entered during the editing of the running sequence to prevent locking a line with an invalid value. After correcting the value, the sequence must be manually resumed.

The "No Data received for 10 sec" or "No data from Acquisition..." messages mean what they say, no data were received from a detector or A/D converter (Colibrick, etc.) for a certain time. It may be caused by several cases:

1. In most cases, there is some problem on the computer - processor overload, interference on the USB bus, time-consuming net search, or backup operations blocking the communication for some time. The error invoked will stop an acquisition or interrupt the sequence.
   Suspected programs are incorrectly set antivirus (continuous checking of file types used by Clarity during data acquisition - raw, prm, audit, tmp should be avoided), programs monitoring files on exchangeable media (i.e. programs for organizing and presenting pictures, music, or video, including some CD/DVD burning programs). One such persisting problem was reportedly solved by removing the Roxio Burning software.
   This will occur more frequently on slow computers, the triggering action may be processor overload or some programs blocking the communication for an extended period.
    
2. In some cases, Windows may suspend the power of the USB HUB in the computer and this unexceptionally causes a loss of connection to connected HW (e.g., Colibrick). Try to check the Device Manager dialog - Universal Serial Bus controllers. Display the Generic USB HUB Properties dialog - Power Management tab. Set Disabled for option Allow the computer to turn off this device to safe power. In case the problem is temporary, sending the method again may solve the problem. If not, disconnect and reconnect the USB HUB.
   The above-mentioned problem with communication was not observed when the USB hub is connected to the USB C connector on the PC.

During acquisition, data are stored in the temporary directory (...\TMP\ $ch1run.raw file ). The data are stored from memory to disk in approximately 1 min intervals. In case the Clarity crashes/freezes during a run, the up to that moment acquired data could be recovered using the Data Recovery ...  command from the Single Analysis window. Note the chromatogram will be created according to the method and parameters specified in the Single analysis (file name and processing parameters), which may be different from the ones used in the Sequence.

During the freeze, it will depend if the thread collecting and storing the data to disk will be still active, with a crash, the data to the last minute before the crash could usually be recovered. In case the computer freezes often, it will be advisable to investigate the cause and try to find a remedy – please do not hesitate to send us the respective diagnostic files. A Memory dump may be helpful for such situation.

Installation

• Installation to program files: In Windows 7, the folder Program files is protected, however, Clarity needs user access to the data and system files. It is not recommended to install Clarity there.

User privileges settings:

• Clarity users must have read/write access to the Clarity system and data files. The default C:\Clarty (C:\ClarityLite) directory inherits the Read Only status from C:\ on administered systems. It is recommended to Install Clarity for the User that will use Clarity under the "As Administrator" option. If not possible, contact your local administrator to change the settings.

Antivirus programs:

Antivirus programs usually do not interfere with Clarity functionality. But two areas may pose problems for the correct functioning of Clarity:

1. Antivirus is causing processor overload in certain situations, which may leave insufficient memory resources for Clarity.
2. Antivirus continuously monitors files frequently updated by Clarity (.raw, .audit, etc.), which may be unjustifiably marked as a threat to the PC.

Windows Updates:

Automatic Windows updates are in the default settings that force the unattended computer to restart regardless of running programs - only a warning message will appear. Please note that the first two options (Automatic updates or Download updates) may result in a forced computer restart.

We recommend installing and operating Clarity on a PC with updated OS, only the forced restarts pose a potential problem to Clarity.

In Windows 10 and 11, it is not possible to forbid the updates; just pause updates for a short period of time and install them manually to avoid forced restarts. Go to Settings - Windows Update - Advanced Options - Pause Updates

In Windows 7, 8.1 go to Control Panel - System and Security - Windows Update- Change settings.
Choose one of the options for automatic updates:

• Never check for updates.
• Check for updates, but let me choose whether to download or install them.

Ask your local administrator to choose one of the options described above on administered systems.

Control Modules and Tools

User Account Control (UAC) needs to be disabled during the installation of some control modules (CTC PAL, Shimadzu LC systems)

To install the CTC PAL autosampler or Shimadzu LC-10/20 system it is necessary to disable the UAC (User Account Control) during installation, otherwise, it will be unsuccessful. Similar problems were reported for the installation of the Agilent 1100 system, again the UAC disabling helped.

See also Table of compatible Windows OS, Clarity SW and DataApex Hardware

When Clarity (Lite) is started, an error message stating "Missing HW key" may appear. This issue arises when the required hardware key is not detected by the system.

If you encounter any problems, the first step is to check the USB port the key is plugged into. Try moving the HW key into a different USB port on the PC or another PC. Most issues are related to the USB port's energy-saving settings in Windows or a faulty USB port.

The Rockey USB ND does not require any separate driver installation; once plugged into a USB port, all necessary drivers are automatically installed. For problems encountered in the case of older keys, see the section below.

Make sure that the LED diode in the key is steadily lit. If it is blinking or it is not lit at all, the hardware key may be faulty, and you will need to send it to us for inspection. Please contact us at sales@dataapex.com in such case.

Old HW key types

The older HW key types require drivers to be installed prior to their use. The Rockey USB/LPT and Sentinel USB/LPT HW keys might not be functional due to installation of a wrong driver. This situation occurs in the case this HW key was connected to the PC before the installation of the correct driver by Clarity. This can be solved by manually uninstalling the wrong driver, restarting the PC, and installing the correct one. To do so, the installer of the drivers can be found in the Clarity\BIN\HW_DRIVERS\ subfolder.

Sentinel HW keys cannot be used with the current Clarity release.

Rockey USB	Rockey LPT	Sentinel USB	Sentinel LPT
	Rockey LPT key can be used only with LPT1 only on board LPT ports, not the ports on PCI cards

Yes, since Clarity 8.0 you can work with up to 10 internal standards.

If you experience a long delay when downloading the Clarity installer from www.dataapex.com and the download process seems to hang when it's almost complete, it's possible that your anti-virus software is scanning your web communication and downloads for viruses, which can cause the delay. 

The delay duration depends on the file size and anti-virus SW used.

If your PC and chromatograph are connected directly via LAN and autodetect is not possible, continue with the following procedure:

• You need a cross-over ethernet cable (a straight-through cable is not recommended).
• Open Windows Settings - Network & Internet - Ethernet tab - Change adapter options - right mouse click on the Local Area Connection and choose Properties.
• In the Local Area Connection Properties, choose Internet Protocol Version 4 and click the Properties button.
• Check the radio button in the Internet Protocol Version 4 (TCP/IPv4) Properties window. Use the following IP address.
• Fill in the IP address. 
  • The first three positions define the network and must be the same as in the device's IP address. 
  • The last position defines the device and must be unique within the network, so do not use one of the connected instruments. Eventually, other Ethernet boards within the computer must not share the same network.
• The subnet mask needs to be 255.255.255.0

The peak detection algorithm used in FC-GP can be explained using the figure below. The red color is the signal, and the blue color is the derivative of the signal (basically a slope at that moment). The axis on the left is shown in the units of the derivative. For illustration, there are two green vertical lines at 2 and -2 (let us assume the slope has a start value of 2 and an end value of 2).

The first peak is collected when the derivative raises over limit 2 (first upward black line). The peak is collected through the peak apex (even before the derivative falls below 2) and is still collected when the derivative falls below -2. Then, it rises, and the peak-end is triggered when the derivative increases from some -4 above -2 (which is the negative of the end limit). If the derivative on the peak-end never falls below -2, the fraction will never end (until the end of the collection interval).

It is possible to schedule a task that will run Clarity with defined parameters automatically starting a sequence. Proceed as follows:

1. Prepare a batch file (clarity.bat) to perform the required tasks using the command line parameters
   The batch should contain the following line (example):

   • start C:\Clarity_Demo_304\Bin\Clarity.exe i=2 u="Administrator" psw="" seq=C:\Clarity_Demo_304\FC\FC3.seq run_seq=2

   Explanations:

   • start C:\Clarity.exe will start the Clarity in the specified directory
   • i=2 will open the desired instrument (2)
   • u="Administrator" psw="" will open it as a specified user with a specified password (essential, otherwise it stay waiting for this input)
   • seq=C:\Clarity_Demo_304\FC\FC3.seq specifies the sequence to run
   • run_seq=2 starts the sequence on instrument 2
2. Prepare the sequence to be started
   The sequence can contain just one line with the start-up method, or some standards/samples can be defined in the following rows. In the start-up method, define to switch the lamp on and flush the system as required to equilibrate.
3. Use the Task Scheduler
   Set the clarity.bat to be started at a defined time and date. Open the "Task Scheduler" Windows app. Use the advanced properties of the task to fine-tune the scheduling.
   Set the task to start when you are logged on only, and when leaving the PC, do not log yourself off. Remember, Windows Update must not run there. It may log you out and restart the PC.

The path in the batch file can differ according to Clarity version you use (version up to 6.2 - start C:\Clarity_Demo_304\Clarity.exe i=2 u="Administrator" psw="" seq=C:\Clarity_Demo_304\FC\FC3.seq run_seq=2).

Yes, Clarity can be connected to any LIMS by importing/exporting text files. Results can be exported in various formats to the LIMS, and the sample info can be imported from a TXT file into Clarity Sequence, which you intend to process.

Please see our manual describing the Clarity cooperation with LIMS: Cooperation with LIMS systems.

An upgrade to the new major Clarity version (change in the first number before the dot) is paid and requires a new user code. Please refer to your price list under p/n C500 (C400/C591). All minor version updates (change in any number after the first dot) are provided free of charge and do not require a new user code. 

For more details, please refer to Clarity Upgrade Policy.

The installer of the current release version can be downloaded directly from the station, or from our websites.

Most chromatography systems use a proprietary data format (the main reason is the belief that it ensures data integrity for GLP-related requirements). To open and process such chromatograms in Clarity, they must be first exported from the original software into a suitable format. The most commonly used formats are AIA (.cdf files) or ASCII (.csv, *.txt, *.asc, and others). Clarity can import such files (only the chromatogram data, not the integration method or result tables) and process them using the current instrument method.

Chemstation

• The export is available with full menus active in the Data Analysis view (menu File, command Export file, AIA file....). Due to the way the Chemstation exports the files (they are always named signal01.cdf and stored in user-named folders; batch export is not supported), the processing is not very convenient and will be quite laborious for a large number of files.
• The export of DAD data is even more complicated, if not impossible (you will have to export each wavelength separately and combine them to the format that can be imported to Clarity).

EZ Chrom

• The chromatograms can be exported during processing, in the Advanced Method Options, Export tab for option Chromatogram the AIA and ASCII formats can be selected.
• The ASCII  *.asc file format is supported by Clarity both for chromatograms and 3D data. AIA files can be used as well.

We release upgrades (major versions) every 1–2 years. There are also 2–3 updates (minor versions) between upgrades.

This situation is unpleasant because the loss of the HW key equals the loss of the license. The software and a new HW key must be repurchased.

We include warning labels attached to HW keys in each delivery.

A user needs to fill out the "Registration of a university package" form that is available on our website. A description of the registration procedure is a part of Clarity Offline delivery.

If you have bought an extension or control module license, you will get a new user code for the latest SW version and have to use the version compatible with the user code (if you have it, there is no need for reinstalling).

On top of that in the case of a new control module, reinstallation depends on how you installed Clarity originally (typical, full, or custom installation). If you miss any control module in the System Configuration window, you must reinstall Clarity.

Only one Clarity software can be run on one PC.

We can offer Clarity (Lite) with analog data acquisition for each chromatograph and A/D converter Colibrick. Chromatographs/detectors need a standard analog output and means for local control, e.g., the instrument's keyboard. As a part of this basic solution, we also offer elementary synchronization with any autosampler.

An Add-on Instrument is a software extension required for each additional chromatograph (new independent time base) connected to the Clarity software. Each Add-on Instrument can be ordered as p/n C55. A maximum of 3 add-on instruments can be added to each Clarity.

A Clarity Control Module is an optional software module that enables autosampler, GC, GC-MS, HPLC/CE, or HPLC-MS control. Clarity can control chromatographic hardware listed in the datasheet List of currently controlled instruments (D004). Detailed descriptions of control options can be found on our website or in the corresponding control manuals.

Clarity Offline is a special version for data processing only where no real device is connected. It is to be installed on a different PC than a version for data acquisition. S/N for the offline version always starts with 98-xxxxx.

The sample rate needs to be set to provide enough points to describe the peaks of interest adequately. It is recommended that at least 30 points be reached per the narrowest peak width. The default value for DataApex's A/D converters is 10 Hz. This is suitable for most HPLC and packed column GC applications. The capillary GC and CE applications may need higher sample rates.

Accordingly, the Global Peak Width parameter must also be amended to match the sampling rate.

For the Gow-Mac GC chromatograph, use the asymmetrical connection as shown in the picture below.

Connect Brown wire (pink tubular end sleeve) to terminal (+) and white wire (grey tubular end sleeve) together with yellow wire (shielding) to terminal (-).

Do not connect anything to the terminal marked D in the picture, it may cause damage to the A/D converter. Set also the Signal Range at the Method Setup Acquisition tab to the lowest possible value.

Dani Master GC

In case your Master GC has an older firmware that supports an older version of Clarity than you have installed it is possible to use older drivers in newer Clarity (up to 8.1). Proceed as follows:

• Copy CswDaniSpAMasterGC.dll and MasterGCControl.dll from the previous Clarity version and rewrite them in your current Clarity installation directory.

It is not possible with Clarity version 8.2 and newer because of our internal policy.

Dani Master DHS

Dani Master SHS

Most probably, yes, the list contains only directly controlled autosamplers. In other words, those where it is possible to set the position and injection method using a computer. Nevertheless, Clarity allows basic synchronization (allow injection and start data acquisition) with arbitrary autosamplers equipped with appropriate control output and input. 

For more information about AS connection, refer to Chapter 6 (Connecting Autosamplers) in the Getting Started manual. 

Yes, you can. There are two possible intentions of using the sequence table for starting the acquisition:

1. Using sequence for manual injections
   You could define parameters for a series of injections in advance in a sequence table and then inject them one by one manually. In such case, the start must be external (individual runs in sequence cannot be started from Clarity). 
2. Using sequence for automatic injections without an autosampler
   In such case, the sequence must be in the active mode (set through Sequence Options dialog). Sequence sends a command to the sampler (over a serial line or by digital output) and waits for the start signal from the detector (again over the communication line or digital input). Without an autosampler, it is possible to start the acquisition by using the digital input and output specified in Ext. Start Dig. Input and Ready Dig. Output section of the System Configuration dialog.

How to set digital input and output to start the sequence without an autosampler?

• In case the injection is performed by some controlled valve or instrument (typically EAS analyzers) not supporting the Injection marker by digital output, the common solution when using the DataApex's A/D board is to interconnect the digital output set for Ready Out signal directly to the digital input set for Start In command. The digital input on the instrument starting the next run will be connected in parallel. With a controlled valve, the injection is then performed during the actual run by switching the valve (or valves) from the Clarity Event Table.

Events must be set in the Event Table accessible from the Method Setup dialog.

• In case no A/D board is used and the devices are not offering those digital inputs and outputs (for example with Agilent GC 5890), the suggested workaround will be to use the DataApex Virtual Digital Input Output Loop (auxiliary device, requires A24 LC or A23 GC Control license) to simulate the input/output needed - (those are virtually interconnected).

For more detailed info refer also to Clarity Getting Started manual, chap. 6.