FAQ

Clarity Chromatography Software supports two main ways to connect instruments:

1. Digitally Controlled Instruments – Clarity communicates with the instrument directly, can control it, and collects data digitally.
2. Analog Instruments – The instrument sends an analog voltage signal, which is digitized by a A/D converter Colibrick, but Clarity cannot control the instrument except for some basic synchronization – all settings must be configured manually on the device itself.

Each option offers a different level of integration, automation, and data quality.

1. Digitally Controlled Instruments – Full Control and Communication

These instruments are fully integrated with Clarity using a digital interface (RS232, USB, LAN, etc.). Communication is bi-directional: Clarity can send commands to the instrument and receive data, status, and error messages.

Key benefits:

• Control instrument parameters directly from Clarity (e.g., flow, temperature, gradient, wavelength).
• Start/stop the device or switch valves remotely.
• Receive feedback from the instrument (diagnostics, status, alerts).
• Synchronize the whole workflow, including autosamplers and detectors.
• Automate complex sequences (startup, conditioning, analysis, shutdown).
• Audit trail: All settings used during the analysis are logged automatically.

This setup is ideal for labs that need high efficiency, traceability, and regulatory compliance.

2. Analog Instruments – Signal Only, No Control

Analog instruments do not communicate with Clarity. Instead, they generate an analog voltage signal (typically 0–1 V or 0–10 V), which is digitized by a A/D converter Colibrick before being processed and displayed in Clarity.

These instruments provide data only — no direct parameter control or feedback is possible, though basic synchronization (e.g. start signals, digital outputs) is supported.

What you can do:

• Acquire the detector signal through an A/D converter.
• Trigger external devices (e.g., autosamplers) via digital outputs.
• Start acquisition using an external start signal.
• In some cases, control gradients via analog output using Zebrick D/A converter.

What you cannot do:

• Set or change any instrument parameters from Clarity.
• Monitor instrument status or errors.
• Synchronize methods or workflows.
• Automatically log instrument settings.

All adjustments (flow, temp, wavelength, etc.) must be done manually on the instrument's physical interface.

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
• Testa Flowmeter control module and 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.

Clarity is a 32-bit process, which means it can use the max of 2GB RAM, but if you use more than one demanding instrument, it can still be beneficial to have 8 GB RAM, so the PC has enough RAM left for OS and other apps.

If you get the "Out Of Memory" error, e.g., when opening measured chromatograms while running a sequence, it may be caused by using a particular method, which has been saved over and over again due to some modifications. Every saving of such a method results in creating another method version (the number of versions is displayed at the top of the Method Setup dialog behind the method name as "- #number"). These versions increase the Method file size; memory can be depleted when such a large method is used, forcing the software to misbehave.

As a remedy:

• Try to save the method using the command Save As under a new name. This will save your method without previous versions, decreasing the file size.
• Do not use "Open chromatograms in Overlay" when running a Sequence.
• Do not open resulting chromatograms when Sequence is running (Disable the checkbox in the Open column).
• Limit the number of chromatograms included in printing of a summary report.

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.

It is not possible to install Clarity on Windows 10 LTSC releases, where .NET Framework version 4.8 or newer cannot be installed (this should apply to Windows 10 Enterprise LTSC 2015). Clarity installation requires .NET Framework version 4.8, introduced as part of Windows updates in 2019 (Windows build 1903).

Importantly, DataApex cannot guarantee complete Clarity functionality in LTSC Windows releases, as they are not among supported OS (only OS with the latest updates is fully supported) and are not properly tested with Clarity.

All Software and Hardware requirements are listed here. You can test whether it is possible to install Clarity to the system by downloading and installing Clarity Demo.

You can read your software version from the software main window in the Help – About menu.

Most problems with Colibrick are related to the USB power supply. So if USB hub is used, we recommend using a hub with an external power source.

It's important to note that Colibrick is sensitive to communication delays. These delays can be caused by issues with the computer's hardware or software, such as processor overload, low RAM memory or running processes blocking the processor or communication lines. If there is no communication for more than 10 seconds, an error message will be displayed, such as "No data from Acquisition" or "No data received for...". This will cause the acquisition to stop and the running sequence to be interrupted. If the problem is temporary, resending the method may solve the problem. Otherwise, try disconnecting and reconnecting the USB hub.  

To check for issues, use the Task Manager to inspect the processor load and processes consuming a large amount of CPU time or memory. Programs that can cause issues include incorrectly set anti-virus programs that continuously check file types used by Clarity during data acquisition. To avoid this, disable the *.raw, *.prm, *.audit, and *.tmp file types for scans. Other programs that monitor files on exchangeable media, such as programs for organizing and presenting pictures, music or video may also interrupt the acquisition. It's also important to note that any actions started during the acquisition, such as printing to a slow USB or network printer, large file transfers over network or USB, connecting or disconnecting USB devices, computer entering sleep mode can cause the acquisition to be interrupted.

Finally, it's worth noting that the communication problem with Colibrick can be avoided by connecting the USB hub to the USB C connector on the PC.

This usually happens when upgrading Clarity from an earlier version. The IQ program checks all registered files and, if they are no longer used in the new version, will cause the check to fail. However, the station will usually function correctly.

To get Passed for IQ results, it is necessary to:

1. Remove the previous Clarity installation using the Uninstall Clarity command from the Windows Start menu - All Programs - Clarity program group.
2. In case you can still see some *.dll files in C:\Clarity\Bin (since 7.0), delete them manually.
3. Install Clarity again.

 The Uninstall Clarity command will remove the program files only, leaving the configuration and data intact.

In Clarity versions prior to 7.0, *.dll files were present in the C:\Clarity root directory.

Clarity stores the IP address of the device detected during autodetection in the configuration and if it changes, it is unable to communicate with the device. Some devices use IP adress assigned by DHCP server in default settings.

If the system is connected directly to the computer or via a switch, it is necessary to set static IP addresses in the devices and in the LAN card in the computer (preferred solution). Refer to the device manual or contact device manufacturer/supplier for how to change the device setting to a static IP address.

If the system is connected directly to the computer via router, it is possible to use DHCP IP address assignment, but you must ensure that the assigned IP addresses do not change. The same applies for connections via an internal network, where the cooperation of the network administrator is required to set the IP address.

The error message pops up after the start of Clarity.

This problem is caused by the wrong configuration file saved in Clarity\cfg. The most common reason is that the computer was shut down while Clarity was running. Normally, Clarity saves the clarity.cfg file when exiting, but when the computer is shut down while doing this, the clarity.cfg file may be corrupted and cannot be used in Clarity next time it is opened.

The corruption of the clarity.cfg file may happen in numerous ways. Here are the two most common situations:

• When the computer is switched off while the Clarity is running, e.g., while experiencing some fluctuations in the power system.
• When the computer is switched to the sleep mode, while Clarity is open, but not running (e.g. during lunchtime). While the analysis in Clarity is running, Clarity blocks switching to the Sleep mode, but without it, it can't do so. In sleep mode, the computer loses the communication between Clarity and the A/D converter and/or hardware key, which may result in destroying the configuration.

All data, such as methods, sequences, data files, calibrations, etc. are saved on demand and are not corrupted when a similar situation arises. The clarity.cfg file holds the information of the Directories and the System Configuration settings, that are lost, so they must be set manually once more.

To repair the damage, follow this process:

1. Open the System Configuration dialog and configure your system manually (eg. add detectors, LCs, GCs, valves and so on to the configuration), fill in their settings and distribute them to particular instruments.
2. Close the System Configuration dialog by clicking OK.
3. If you had the Directories dialog set before, use the System - Directories command from the Clarity window to set it once more. Then, close the dialog.
4. Open the Instrument. Load the desired project to the Instrument; Default clarity.cfg file has the Work1 directory set as the project directory, you have, most probably, created your own project before the shutdown. Use the File - Project command, select the appropriate project from the list and press the Open button.
   Note: You might get the information similar to "the current method was prepared on a different configuration. Some parameters will be used in default format" if you opened and then saved the method after the clarity.cfg file was corrupted, there might be necessary to check/set some parameters, mainly on the Method Setup - Acquisition and Method Setup - Measurement tabs.
5. Exit the station. The clarity.cfg file was now saved with the correct settings of the configuration.
6. You can back up this configuration to some other directory to prevent the manual settings if the problem occurs again.

The station should now be in the configuration as before the failure.

To prevent this from happening in the future if the reason was the sleep mode follow the procedure:

• In Windows 10 and 11 invoke Settings - System - Power & Sleep - Additional power settings - Choose when to turn off the display - Change advanced power settings and set Sleep after item and Hibernate after to "Never". Apply changes and use OK to exit this dialog.

• In Windows 7, 8.1 go to Control Panel - Hardware and Sound - Power Options - Edit Plan Settings to change the settings.

Corruption should be prevented in the future. Of course, if it was caused by another reason, such as instabilities in the power network, only a good stabilized backup power source and backing up your configuration may help.

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.

LAN communication

General issues

For LAN communication, one of the 1100/1200 modules must be equipped with a LAN communication card inserted in the MIO slot on the backside of the module (do not mistake it for the CAN connectors used for the internal system communication, using the same RJ45 connectors).

The original board supported by Agilent is a G1369A LAN Interface described in Agilent G1369A LAN Interface User Manual (Agilent P/N G1369-90000).

We don't support J4100A JetDirect card (alternative to HP JetDirect Print Servers 600N/400N/500X/300X) nor guarantee the functionality.

Connecting single PC directly with 1100/1200 system

In case you need to connect the PC directly with the 1100/1200 system using a LAN card, see chapter 3.3.4 Single PC & network connection in the Agilent 1100 manual.

GPIB Communication

Communication using GP-IB card could not be established

When the communication with the Agilent 1100/1200 system by the GP-IB card could not be established, even if all the parameters are set correctly and the Agilent IO Libraries report the module as connected on the used ID address, then it is necessary to check the Agilent IO Libraries.

The Agilent IO Libraries must be closed (Use the Exit command) before the communication with Clarity can be established.

During the installation of the Agilent IO Libraries, they are added to the programs to be started automatically at the system start. It is necessary to disable this function because they could not run simultaneously with Clarity.

• In Windows XP, Vista and 7 - remove them from the  Windows Start menu, Programs (All Programs), and Startup group.
• In Windows 8, 10 and 11 - start the Task Manager (display more details in the window) and locate the Start-up tab. Disable them.

After the communication was lost, it could not be reestablished

When using the GP-IB USB converter, it may be necessary to disconnect the converter from the PC to clear the communication buffers. As the USB can be powered even during a computer shutdown, the shutdown and restart may not help.

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.