<h3><strong>Introduction</strong></h3><p>In chromatographic data analysis, efficient handling of measured chromatograms is crucial for productivity and accuracy. This technical guide provides a step-by-step explanation of how to open and manage chromatograms that were measured as part of a sequence using <a target="_blank" rel="noopener noreferrer" href="https://lcms.labrulez.com/products/999"><span><strong>Clarity Chromatography Software</strong></span></a>. The procedures outlined are based on a demonstration video from DataApex’s official YouTube channel and are tailored for users seeking a streamlined analytical workflow.</p><h3><strong>Tools and Software</strong></h3><ul><li><strong>Software</strong>: Clarity Chromatography Software by DataApex</li><li><strong>System Requirements</strong>: PC with sufficient RAM to handle multiple chromatograms in memory</li><li><strong>Prerequisites</strong>:<ul><li>A completed measurement sequence</li><li>Access to the Sequence and Chromatogram windows in the software</li></ul></li></ul><h3><strong>Method 1: Opening Chromatograms from the Sequence Window</strong></h3><h4><strong>Step 1: Navigate to the Sequence Window</strong></h4><ul><li>Open the <i>Sequence</i> window within Clarity.</li><li>Load a previously measured sequence.</li></ul><h4><strong>Step 2: Expand the Status Cell</strong></h4><ul><li>Locate the <strong>status cell</strong> in a row corresponding to a finished measurement.</li><li>If the row produced chromatograms, the status cell is expandable.</li><li>Click on the <strong>arrow icon</strong> in the status cell to reveal a local menu.</li></ul><h4><strong>Step 3: Select Chromatograms to Open</strong></h4><ul><li>In the local menu, select one or more chromatograms you wish to open from that row.</li><li>The chromatograms will open in <strong>overlay mode</strong>.</li></ul><h4><strong>Note on Overlay Mode</strong></h4><ul><li>Overlay mode is <strong>automatically enabled</strong> when multiple chromatograms are opened using this method.</li><li>By default, <strong>a maximum of 20 chromatograms</strong> can be opened in overlay mode.</li><li>If more chromatograms are selected, the earliest one opened will be automatically closed.</li></ul><h4><strong>Optional: Adjust the Overlay Limit</strong></h4><p>To change the default overlay limit:</p><ol><li>Go to the <strong>Instrument window</strong> menu.</li><li>Navigate to: <code>Setting</code> &gt; <code>User Options</code></li><li>In the <strong>General tab</strong>, locate the <strong>Limit</strong> section.</li><li>Adjust the maximum number of chromatograms allowed in overlay mode.</li></ol><blockquote><p>⚠️ <strong>Recommendation</strong>: Set a reasonable limit based on your system’s memory capacity. Opening too many chromatograms simultaneously can lead to performance issues.</p></blockquote><h3><strong>Method 2: Opening All Chromatograms from the Chromatogram Window</strong></h3><h4><strong>Step 1: Navigate to the Chromatogram Window</strong></h4><ul><li>Ensure that no chromatograms are currently open, or manually close them if needed.</li></ul><h4><strong>Step 2: Use the File Menu</strong></h4><ul><li>Go to the <strong>File</strong> menu.</li><li>Select <strong>Open Chromatograms from Sequence</strong> to invoke the file selection dialog.</li></ul><h4><strong>Step 3: Select and Confirm</strong></h4><ul><li>Choose the desired <strong>measured sequence</strong> from the dialog box.</li><li>Confirm the selection.</li></ul><p>All chromatograms associated with the selected sequence will now open simultaneously in the chromatogram window.</p><h3><strong>Conclusion</strong></h3><p>Clarity Chromatography Software offers flexible options for opening chromatograms measured in a sequence. Whether accessed from the Sequence window for selective viewing or from the Chromatogram window for batch loading, both approaches enhance the user’s ability to review data efficiently. By adjusting overlay settings to match system capabilities, users can tailor the experience to their specific workflow needs.</p><blockquote><p>For further video tutorials and advanced tips, visit the <a target="_blank" rel="noopener noreferrer" href="https://www.youtube.com/@DataapexPrague"><strong>DataApex YouTube Channel</strong></a>.</p></blockquote>

 How to open chromatograms from a sequence 

<h3><strong>Introduction</strong></h3><p>The <a target="_blank" rel="noopener noreferrer" href="https://lcms.labrulez.com/products/999"><strong>Clarity Chromatography Software</strong></a> provides advanced tools for managing chromatographic sequences. Correct configuration of <strong>sequence options</strong> is crucial, as it defines how the sequence table operates, how runs are executed, and how results are stored. This article provides a step-by-step guide to setting up sequence options, based on an instructional video demonstration.</p><h3><strong>Accessing the Sequence Options Dialog</strong></h3><ol><li>Open the <strong>Sequence Window</strong>.</li><li>Select the <strong>Options</strong> icon from the toolbar, or choose the <strong>Options</strong> item from the Sequence menu.</li><li>The <strong>Sequence Options dialog</strong> will appear, containing several configurable sections.</li></ol><h3><strong>Sequence Description</strong></h3><p>At the top of the dialog, you will find a <strong>Description field</strong>. This is a free-text area where you can enter notes or identifiers for the sequence. Although optional, it is useful for documenting specific experiment details.</p><h3><strong>Sequence Mode</strong></h3><p>This section controls how Clarity handles the start of a sequence:</p><ul><li><strong>Passive Mode</strong><ul><li>Clarity waits for an external start signal (e.g., from a connected device).</li><li>Commonly used for <strong>manual injections</strong> or with <strong>uncontrolled autosamplers</strong>.</li><li>The run begins when triggered by an external event, such as turning a manual injection valve.</li></ul></li><li><strong>Active Mode</strong> <i>(default option)</i><ul><li>Clarity manages the entire process.</li><li>It waits for all devices to be ready, then signals the autosampler to inject.</li><li>Once injection is complete, the run starts automatically.</li><li>Suitable for the majority of automated workflows.</li></ul></li></ul><p>For more detailed instrument-specific settings, refer to <strong>Chapter 6 of the Getting Started Manual</strong>.</p><h4><strong>Idle Time in Active Mode</strong></h4><p>You can configure a <strong>delay (idle time)</strong> between the end of one run and the start of the next injection.<br>This feature is useful if:</p><ul><li>Devices require additional stabilization time.</li><li>Too many commands at once could cause communication issues.</li></ul><h3><strong>Sequence Row Selection</strong></h3><p>This field allows you to specify which rows in the <strong>sequence table</strong> will be executed.</p><ul><li>The software automatically sets the corresponding checkboxes in the <strong>Run column</strong>.</li><li>You may still manually adjust them afterwards.</li></ul><h3><strong>Counter Variable Settings</strong></h3><p>The <strong>counter variable</strong> can be configured here to increment automatically during the sequence.</p><ul><li>The counter can be used for labeling runs or files.</li><li>It increments with every new run in the sequence.</li><li>Depending on configuration, it may or may not reset.</li></ul><h3><strong>File Name Conflict Resolution</strong></h3><p>When multiple analyses are initiated from one row, <strong>file naming conflicts</strong> may occur. Two options are available:</p><ul><li><strong>Automatic (default)</strong><ul><li>Clarity appends a <strong>vial or injection variable</strong> to the file name, preventing duplication.</li></ul></li><li><strong>Manual</strong><ul><li>The user resolves conflicts manually before saving.</li></ul></li></ul><h3><strong>Calibration and Sequence Usage</strong></h3><p>This section allows you to define the type of <strong>calibration cloning</strong> used within the sequence.</p><ul><li>For a full explanation of calibration settings, refer to the<a target="_blank" rel="noopener noreferrer" href="https://www.youtube.com/watch?v=aX-BwAXb0dI&amp;list=PLSPrHzY76_FRTmmtEUbaaQj2NrrGM3PCC"> <strong>Calibration playlist</strong></a> provided by Clarity.</li></ul><h3><strong>After Sequence Is Finished</strong></h3><p>At the end of the sequence, you can set a <strong>shutdown method</strong> for devices.</p><ul><li>For example, powering down pumps or turning off detectors.</li><li>A detailed explanation is available in the related tutorial: <i>“</i><a target="_blank" rel="noopener noreferrer" href="https://www.youtube.com/watch?v=B2NHqaNf05Q"><i><strong>How to Shut Down Devices After the Sequence Is Finished</strong>.</i></a><i>”</i></li></ul><h3><strong>Saving and Applying Settings</strong></h3><p>Once configuration is complete:</p><ol><li>Click <strong>OK</strong> to save the sequence options.</li><li>The parameters will apply immediately to the open sequence file.</li></ol><h3><strong>Example Configuration (from video demonstration)</strong></h3><ul><li><strong>Mode:</strong> Active</li><li><strong>Idle Time:</strong> 5 minutes</li><li><strong>Rows Executed:</strong> Only rows 2 and 4</li><li><strong>Row 4:</strong> End vial edited to allow multiple measurements</li><li><strong>File Name Conflicts:</strong> Solved automatically by appending the vial variable</li><li><strong>Counter Variable:</strong> Starts at 5, increments with each run, never resets</li></ul><h3><strong>Conclusion</strong></h3><p>Configuring sequence options in <strong>Clarity Chromatography Software</strong> ensures smooth operation, consistent data handling, and efficient automation. By mastering the settings for <strong>sequence mode, idle time, file naming, calibration, and shutdown methods</strong>, analysts can tailor workflows to specific laboratory requirements.</p><blockquote><h4><strong>For further guidance, users are encouraged to consult:</strong></h4><ul><li><strong>Chapter 6 of the Getting Started Manual</strong></li><li><a target="_blank" rel="noopener noreferrer" href="https://www.youtube.com/watch?v=aX-BwAXb0dI&amp;list=PLSPrHzY76_FRTmmtEUbaaQj2NrrGM3PCC"><strong>Calibration tutorials</strong></a></li><li><a target="_blank" rel="noopener noreferrer" href="https://www.youtube.com/watch?v=B2NHqaNf05Q"><strong>Device shutdown video guide</strong></a></li></ul></blockquote>

How to set the Sequence Options in Clarity SW

<h3><strong>Introduction</strong></h3><p>Efficient data handling after chromatographic runs is essential for ensuring accurate evaluation, reporting, and workflow automation. <a target="_blank" rel="noopener noreferrer" href="https://gcms.labrulez.com/products/999"><strong>Clarity Chromatography Software </strong></a>provides a set of <strong>post-run actions</strong> that can be configured to streamline operations. This article explains each available function, outlines the configuration steps, and demonstrates how these options can improve analytical productivity.</p><h3><strong>Accessing Post-Run Actions</strong></h3><p>Post-run settings are available in two main areas of Clarity:</p><ul><li><strong>Single Analysis Tab</strong> – where actions can be configured for individual runs.</li><li><strong>Sequence Table</strong> – where post-run actions can be applied across multiple samples.</li></ul><p>By default, many post-run columns are hidden in the sequence table. To enable them:</p><ol><li>Open the <strong>Setup Columns</strong> dialog.</li><li>Locate post-run actions in the <strong>Hidden Columns list</strong> (at the end).</li><li>Display selected columns for easier configuration.</li></ol><h3><strong>Categories of Post-Run Actions</strong></h3><h4><strong>1. Printing (Covered Separately)</strong></h4><p>Printing-related actions are documented in detail in the dedicated guide <i>“</i><a target="_blank" rel="noopener noreferrer" href="https://www.youtube.com/watch?v=WuTsgG894cI"><i><strong>How to Print a Report from Sequence</strong></i></a><i>”</i>. They will not be discussed here.</p><h4><strong>2. Data Opening Options</strong></h4><ul><li><strong>Open</strong> – Opens the finished chromatogram directly in the <strong>Chromatogram Window</strong>.</li><li><strong>Open in Calibration Window</strong> – Loads the chromatogram into the <strong>Calibration Window</strong>, facilitating immediate calibration adjustments.</li></ul><h4><strong>3. Exporting Data</strong></h4><ul><li><strong>Export Data</strong> – Exports result tables and other analytical outputs according to predefined export settings.<ul><li>To configure:<ul><li>Go to <strong>Instrument Window → Settings → Export Data</strong>.</li><li>The <strong>Export Data Settings</strong> dialog allows customization of output formats and locations.</li></ul></li><li>By default, exports are saved in the same directory as chromatogram files, using identical filenames.</li></ul></li></ul><blockquote><p><strong>Important:</strong> Chromatograms must be opened in the <strong>Chromatogram Window</strong> for proper export. The software exports the data tables visible in that layout.</p></blockquote><h4><strong>4. Chromatogram Export Formats</strong></h4><p>Four dedicated columns in the sequence allow exporting chromatograms into different file formats.</p><ul><li>Exported files contain only <strong>header information</strong> and <strong>raw data points</strong> used to construct chromatograms.</li><li>This enables seamless integration with third-party tools or archival systems.</li></ul><h4><strong>5. Running External Programs</strong></h4><p>Three columns are available for <strong>post-run execution of external applications</strong>.</p><ul><li>These can be configured to trigger scripts, data processors, or laboratory automation tasks after each measurement.</li><li>One practical example is shown in the video series <i>“</i><a target="_blank" rel="noopener noreferrer" href="https://www.youtube.com/watch?v=eE0cxllQJOg"><i><strong>How to Chain Sequence</strong></i></a><i>”</i>, where this feature enables automated multi-step workflows.</li></ul><h4><strong>6. SST (System Suitability Test) Inclusion</strong></h4><ul><li><strong>Include in SST</strong> – Determines whether the chromatogram will be automatically included in <strong>SST evaluations</strong> when opened.</li><li>Ensures compliance and system performance verification without additional manual steps.</li></ul><h4><strong>7. Stored Calibration Preference</strong></h4><ul><li><strong>Stored Calibration</strong> – Defines the default calibration source for a chromatogram.<ul><li>If checked, the software opens the chromatogram with the <strong>calibration stored inside it</strong>, rather than the calibration file originally linked.</li></ul></li><li>Useful for consistency when archived data needs to be re-evaluated under the same calibration conditions.</li></ul><h4><strong>8. Closing Chromatograms</strong></h4><ul><li><strong>Close All</strong> – Closes all previously opened chromatograms after a run.<ul><li>If combined with the <strong>Open</strong> option, Clarity will first close existing chromatograms and then open only the most recent result.</li></ul></li><li>Helps maintain a clean workspace and prevents confusion when working with multiple datasets.</li></ul><h3><strong>Practical Applications</strong></h3><p>By combining these post-run actions, laboratories can:</p><ul><li>Automate routine data exports for LIMS integration.</li><li>Standardize chromatogram handling across teams.</li><li>Ensure compliance with <strong>SST requirements</strong>.</li><li>Maintain an uncluttered and consistent Clarity environment.</li><li>Extend Clarity’s capabilities through integration with <strong>external programs and scripts</strong>.</li></ul><h3><strong>Conclusion</strong></h3><p>Clarity’s <strong>post-run actions</strong> provide analysts with powerful tools for automating workflows, managing data exports, and maintaining compliance. Proper configuration not only improves laboratory efficiency but also reduces manual intervention and potential errors. By leveraging these functions, laboratories can significantly streamline their analytical processes and maximize the software’s capabilities.</p><blockquote><p>For additional demonstrations, consult the official Clarity tutorial series, including <i>“</i><a target="_blank" rel="noopener noreferrer" href="https://www.youtube.com/watch?v=WuTsgG894cI"><i><strong>How to Print a Report from Sequence</strong></i></a><i>”</i> and <i>“</i><a target="_blank" rel="noopener noreferrer" href="https://www.youtube.com/watch?v=eE0cxllQJOg"><i><strong>How to Chain Sequence</strong></i></a><i>”</i>.</p></blockquote>

How post run actions work in Clarity  software

<p><strong>Efficient data handling is essential in chromatographic analysis, particularly in laboratories where high throughput and standardized reporting are required. The </strong><a target="_blank" rel="noopener noreferrer" href="https://lcms.labrulez.com/products/999"><strong>Clarity Chromatography Software</strong></a><strong> offers a feature called </strong><i><strong>post-run settings</strong></i><strong>, which allows specific actions to be performed automatically after a measurement is completed. Among these actions, automatic report generation and printing play a crucial role in ensuring data traceability and immediate availability of results.</strong></p><p>This article provides a structured, step-by-step guide on how to configure Clarity to print reports—either to PDF or directly to a physical printer—immediately after the completion of a measurement sequence.</p><h3><strong>Understanding Post-Run Settings in Clarity</strong></h3><h4><strong>What Are Post-Run Settings?</strong></h4><p>Post-run settings are predefined actions executed automatically once a chromatographic run is finished. These can include exporting results, generating reports, sending notifications, or printing.</p><h4><strong>Location of Post-Run Settings</strong></h4><ul><li><strong>Single Analysis tab</strong>: Applies settings to individual chromatographic runs.</li><li><strong>Sequence window columns</strong>: Applies settings across multiple analyses in a batch sequence.</li></ul><p>For this guide, we focus on the <strong>Sequence window</strong> to automate printing.</p><h4><strong>Materials and Tools Required</strong></h4><ul><li><strong>Clarity Chromatography Software</strong> with post-run functionality enabled</li><li>Configured <strong>chromatogram window</strong> for visualization</li><li><strong>Overlay mode</strong> (optional, for multiple chromatograms)</li><li>Defined <strong>report style</strong> specifying the content and layout of the printed report</li><li>Access to a <strong>printer</strong> (physical or virtual PDF printer)</li></ul><h4><strong>Step-by-Step Procedure</strong></h4><h5><strong>1. Display Hidden Post-Run Columns</strong></h5><p>By default, most post-run settings such as <i>Print to PDF</i> remain hidden.</p><ul><li>Navigate to the <strong>Setup Columns</strong> dialog in the Sequence window.</li><li>Enable visibility for the <i>Print to PDF</i> (or <i>Print</i>) column.</li></ul><h5><strong>2. Prepare Chromatogram Window</strong></h5><p>To ensure all relevant chromatograms are included in a single report:</p><ol><li>Open the <strong>chromatogram window</strong>.</li><li>Confirm no chromatogram is currently active.</li><li>Activate <strong>Overlay Mode</strong>.<ul><li>When enabled, multiple chromatograms can be printed together.</li><li>If disabled, each chromatogram is printed separately.</li></ul></li></ol><h5><strong>3. Configure Sequence Actions</strong></h5><ul><li>In the <strong>Sequence window</strong>, check the <strong>Open</strong> checkbox for each chromatogram to be printed.</li><li>Select <strong>Print to PDF</strong> (or <strong>Print</strong>) on the final row.</li><li>Ensure the correct <strong>report style</strong> is applied in the row where the print action will execute.</li></ul><h5><strong>4. Define Report Style</strong></h5><p>The report style determines the exact content and structure of the printed report.</p><p><strong>a) Edit Report Style</strong></p><ul><li>Click the <strong>Edit Current Report Style</strong> icon from the chromatogram tab.</li><li>Adjust default settings:<ul><li>Change <strong>Signals</strong> to <i>All</i>.</li><li>Set <strong>Tiled By</strong> to <i>Chromatograms</i> (ensures each chromatogram has its own graph).</li></ul></li></ul><p><strong>b) Configure Results Tab</strong></p><ul><li>Switch to the <strong>Results</strong> tab in report style editor.</li><li>Adjust settings:<ul><li>Set <strong>Signals</strong> to <i>All</i>.</li><li>Enable <strong>Summary Table</strong>.</li><li>Check <strong>Word Wrap Long Text</strong> for improved readability.</li><li>Select <strong>Force Inverted</strong> in the <i>Table Layout</i> section (compact format with inverted rows and columns).</li></ul></li><li>Save the customized report style.</li></ul><h5><strong>5. Execute Measurement and Generate Report</strong></h5><ul><li>Start the measurement sequence.</li><li>Upon completion, Clarity automatically generates the configured report.</li><li>The final report will include:<ul><li><strong>Graphs of all chromatograms</strong> (each displayed separately).</li><li><strong>Individual result tables</strong> for each chromatogram.</li><li><strong>Summary table</strong> with wrapped names and inverted layout for compact readability.</li></ul></li></ul><h4><strong>Discussion and Best Practices</strong></h4><ul><li><strong>Overlay Mode</strong> is critical when multiple chromatograms must be combined in a single report. Without it, each run will print independently.</li><li><strong>Report styles</strong> should be tailored to laboratory needs. Including both graphical and tabular outputs ensures clear interpretation of results.</li><li><strong>PDF printing</strong> is recommended for digital archiving, while direct printing can be reserved for physical documentation requirements.</li><li>Periodic review of <strong>report templates</strong> ensures compliance with laboratory reporting standards and regulatory requirements.</li></ul><h4><strong>Conclusion</strong></h4><p>By configuring post-run settings in Clarity, laboratories can automate the generation and printing of chromatographic reports immediately after analysis. This approach streamlines workflows, reduces manual intervention, and ensures consistent documentation across all runs. Proper customization of report styles guarantees that results are presented clearly, whether for internal review, quality control, or regulatory reporting.</p>

How to print a report from Sequence in Clarity software

<p><strong>This article provides a structured explanation of how to create and manage a measurement sequence in </strong><a target="_blank" rel="noopener noreferrer" href="https://lcms.labrulez.com/products/999"><strong>Clarity Chromatography Data System</strong></a><strong> (CDS). It is based on the instructional video “</strong><a target="_blank" rel="noopener noreferrer" href="https://www.youtube.com/watch?v=FWaakYQ2ED8"><strong>How to Prepare a Sequence</strong></a><strong>” and reformatted into a comprehensive technical article.</strong></p><h3><strong>Introduction</strong></h3><p>In chromatography workflows, <strong>sequences</strong> are used to define a set of analytical runs in a structured, automated manner. By carefully preparing a sequence, users can save time, reduce errors, and ensure consistency across multiple injections and vials.</p><p><strong>This guide covers:</strong></p><ul><li>Creating a new sequence in Clarity</li><li>Filling and managing sequence rows</li><li>Configuring multiple injections and vial ranges</li><li>Assigning sample types and calibration levels</li><li>Using fill functions to accelerate sequence preparation</li><li>Saving the sequence for measurement</li></ul><h3><strong>Tools and Software</strong></h3><ul><li><strong>Clarity CDS software</strong> with the sequence editor</li><li>Access to appropriate <strong>methods and sample lists</strong> prepared in advance</li><li>Knowledge of vial numbering and sample IDs for the autosampler</li></ul><h3><strong>Step-by-Step Procedure</strong></h3><h4><strong>1. Creating a New Sequence</strong></h4><ol><li>Open the <strong>Sequence window</strong> in Clarity.</li><li>Click <strong>New</strong> to create a fresh sequence table.</li><li>In the first row, enter the required details, such as:<ul><li><strong>Method name</strong></li><li><strong>Sample name</strong></li><li><strong>File name format</strong> (e.g., change variable from <i>Sample ID</i> to <i>Sample</i>)</li></ul></li></ol><blockquote><p>⚠️ <i>Tip:</i> Values from the first row are automatically copied to new rows, ensuring consistency.</p></blockquote><h4><strong>2. Defining Sequence Rows</strong></h4><ul><li>Check the <strong>Run</strong> box to activate the first row.</li><li>Add as many rows as your application requires.</li><li>In the example case:<ul><li>A total of <strong>four rows</strong> were defined.</li><li>Rows can represent repeated injections from one vial or samples across multiple vials.</li></ul></li></ul><h4><strong>3. Configuring Multiple Injections and Vial Ranges</strong></h4><ul><li><strong>Multiple injections from one vial</strong>:<ul><li>Example: Row 1 → set <strong>Number of injections per vial</strong> = 2.</li></ul></li><li><strong>Defining vial ranges</strong>:<ul><li>Example: Row 4 → set <strong>End vial number</strong> = 7 to cover vials 4 through 7.</li></ul></li></ul><h4><strong>4. Assigning Sample Types and Calibration Levels</strong></h4><ol><li>Mark the <strong>Sample type</strong> for each row.<ul><li>Example: The first three rows are defined as <strong>Standards</strong>.</li></ul></li><li>Assign <strong>Calibration levels</strong>:<ul><li>Enter <i>Level 1</i> in the first row.</li><li>Select the corresponding cells for rows 1–3.</li><li>Use <strong>Fill Series</strong> from the right-click menu to automatically increment levels (1, 2, 3).</li></ul></li></ol><h4><strong>5. Using Fill Down and Fill Series Functions</strong></h4><p>To speed up sequence preparation, Clarity provides convenient functions:</p><ul><li><strong>Fill Down</strong>: Copies a selected cell’s value into the rows below.</li><li><strong>Fill Series</strong>: Automatically generates incremental values across selected cells.</li></ul><p>Example applications:</p><ul><li>Fill down method names, injection volumes, or vial numbers.</li><li>Fill series for calibration levels or sequence numbering.</li></ul><h4><strong>6. Saving the Sequence</strong></h4><p>Once all parameters are set:</p><ol><li>Click <strong>Save</strong>.</li><li>Assign a descriptive sequence name for future reference.</li><li>The sequence is now fully prepared and ready for measurement.</li></ol><h3><strong>Discussion and Best Practices</strong></h3><ul><li><strong>Consistency:</strong> Use “Fill Down” to avoid manual repetition and reduce errors.</li><li><strong>Calibration:</strong> Always double-check calibration levels when working with standards.</li><li><strong>Efficiency:</strong> Plan vial positions and injection counts before building the sequence.</li><li><strong>File Management:</strong> Define a logical file naming convention early to maintain clarity in data processing.</li></ul><h3><strong>Conclusion</strong></h3><p>By following this structured approach in Clarity CDS, laboratory staff can efficiently prepare sequences for chromatography runs. The combination of sequence rows, vial configuration, and automated fill functions ensures faster setup, minimized manual errors, and improved consistency across analytical measurements.</p><p>With a properly saved sequence, the system is fully ready for automated data acquisition and subsequent analysis.</p>

How to create a sequence in Clarity software

<p>The <strong>Sequence Window in </strong><a target="_blank" rel="noopener noreferrer" href="https://lcms.labrulez.com/products/999"><strong>Clarity Chromatography Data System (CDS)</strong></a> is a central tool for planning and executing analytical runs. It allows users to define and control all aspects of sample measurement, including sample identification, injection volumes, calibration settings, and post-run actions. This article provides a detailed explanation of the Sequence Window, its key components, and the functionality it offers, based on an instructional video tutorial.</p><h3><strong>Accessing the Sequence Window</strong></h3><p>The Sequence Window is accessible directly from the <strong>Instrument Window</strong> in Clarity CDS. Once opened, the main feature displayed is the <strong>Sequence Table</strong>, which contains the full overview of all analytical runs.</p><h3><strong>Structure of the Sequence Table</strong></h3><h4><strong>Status Column</strong></h4><ul><li>Displays the <strong>state of each row</strong> (e.g., pending, running, completed).</li><li>All possible states with detailed descriptions are available in the <strong>Help section</strong>.</li></ul><h4><strong>Run Column</strong></h4><ul><li>Determines whether a row will be measured.</li><li>Allows the user to <strong>include or exclude specific analyses</strong> from the sequence.</li></ul><h4><strong>Vial Columns</strong></h4><ul><li>Specify the <strong>sample vials</strong> to be used during the measurement process.</li></ul><h4><strong>Sample and Sample ID Columns</strong></h4><ul><li>Used for <strong>sample identification and tracking</strong>.</li><li>Essential for linking results to the correct sample.</li></ul><h4><strong>Post-Calculation Columns</strong></h4><ul><li>Provide options for performing calculations <strong>after measurement</strong>.</li><li>Useful for automated processing and reporting.</li></ul><h4><strong>Injection Volume Column</strong></h4><ul><li>Directs the autosampler on how much volume should be injected per analysis.</li></ul><h4><strong>File Name Column</strong></h4><ul><li>Defines the <strong>name of the resulting chromatogram file</strong>.</li><li>Recommended: Use <strong>variables</strong> in naming to ensure <strong>unique file identifiers</strong>.</li></ul><h4><strong>Sample Type and Level Columns</strong></h4><ul><li><strong>Sample Type:</strong> Defines the role of the sample in calibration (Unknown, Standard, Blank).</li><li><strong>Level:</strong> Specifies the calibration level for standards.</li><li>If Sample Type is set to <strong>Bypass</strong>, the sampler will not inject on that row.</li></ul><h4><strong>Method Name Column</strong></h4><ul><li>Indicates which <strong>analytical method</strong> will be applied to the run.</li></ul><h4><strong>Post-Run Options</strong></h4><ul><li>Control what happens <strong>after a run is completed</strong>.</li><li>Additional post-run columns are hidden by default but can be enabled in the <strong>Setup Columns dialog</strong>.</li></ul><h3><strong>Toolbar Functions</strong></h3><p>At the top of the Sequence Window, a <strong>dedicated toolbar</strong> provides essential controls:</p><ol><li><strong>File Management &amp; Printing</strong><ul><li>Open, save, and print sequence files.</li></ul></li><li><strong>Editing Tools</strong><ul><li>Modify rows, copy/paste, and manage sequence table content.</li></ul></li><li><strong>Sequence Measurement Tools</strong><ul><li>Start, pause, or stop sequence runs.</li><li>Adjust sequence settings via the <strong>Sequence Options icon</strong>.</li></ul></li><li><strong>Method and Report Style Editing</strong><ul><li>Directly edit the <strong>method file</strong> or <strong>report style</strong> from the selected row.</li></ul></li><li><strong>Sequence Validity Check</strong><ul><li>Verifies that the sequence is properly configured before execution.</li></ul></li></ol><h3><strong>Setup Columns Dialog</strong></h3><ul><li>Provides control over which columns are visible in the Sequence Table.</li><li>Useful for customizing the display according to <strong>workflow requirements</strong>.</li><li>Includes hidden columns related mainly to <strong>post-run operations</strong>.</li></ul><h3><strong>Best Practices</strong></h3><ul><li>Use <strong>descriptive sample names and IDs</strong> for traceability.</li><li>Apply <strong>file name variables</strong> to avoid overwriting chromatograms.</li><li>Perform a <strong>validity check</strong> before running the sequence to prevent execution errors.</li><li>Customize the sequence layout with the <strong>Setup Columns dialog</strong> for clarity and efficiency.</li></ul><h3><strong>Conclusion</strong></h3><p>The Sequence Window in <strong>Clarity CDS</strong> is a powerful feature for managing analytical workflows in chromatography. By providing a structured environment for defining runs, controlling injection parameters, and ensuring calibration integrity, it enhances both productivity and accuracy. Users who master the Sequence Window will benefit from streamlined operations, reliable data, and reduced risk of errors.</p><blockquote><p>For further details, consult additional video tutorials on <strong>Sequence Options</strong> and related Clarity CDS functions.</p></blockquote>

Clarity chromatograhy software: Tutorial - Sequence window - Overview 

<h3><strong>Introduction</strong></h3><p><strong>Signal-to-noise ratio (S/N) is a critical parameter in chromatography for evaluating peak quality and method sensitivity. The</strong> <a target="_blank" rel="noopener noreferrer" href="https://lcms.labrulez.com/products/999"><strong>Clarity Chromatography Data System</strong></a><strong> (CDS) includes tools that allow users to calculate S/N directly from chromatograms. This guide explains the complete procedure step by step.</strong></p><h3><strong>Tools and Requirements</strong></h3><ul><li><strong>Clarity CDS software</strong> with chromatogram visualization enabled</li><li><strong>Chromatogram file</strong> containing peaks of interest</li><li><strong>Result Table</strong> window for displaying calculated parameters</li></ul><h3><strong>Step 1: Determining Noise</strong></h3><ol><li>Navigate to the <strong>Chromatogram → Noise and Drift</strong> menu.</li><li>Select <strong>Noise Evaluation</strong>.</li><li>In your chromatogram, mark an interval that contains only baseline noise (no peaks).</li><li>The software determines the noise value and displays it above the Result Table.</li></ol><h3><strong>Step 2: Configuring the Result Table</strong></h3><ol><li>Right-click inside the <strong>Result Table</strong> to open the local menu.</li><li>Select <strong>Setup Columns</strong> to access the configuration dialog.</li><li>Define a new column:<ul><li><strong>Name:</strong> Enter a descriptive label (e.g., <i>S/N</i>).</li><li><strong>Expression:</strong> Input the formula <i>Height / Noise</i>, where <i>Height</i> refers to the peak height and <i>Noise</i> is the variable determined in Step 1.</li></ul></li><li>Disable the <strong>Calculate Total</strong> option, as it is not necessary for S/N.</li><li>Confirm with <strong>OK</strong> to save settings.</li></ol><h3><strong>Step 3: Viewing Signal-to-Noise Ratio</strong></h3><p>Once configured, the Result Table automatically calculates and displays the signal-to-noise ratio for every detected peak in the chromatogram. This allows rapid assessment of peak detectability and compliance with method validation requirements.</p><h3><strong>Discussion</strong></h3><p>The ability to evaluate S/N directly in Clarity provides several advantages:</p><ul><li><strong>Automation:</strong> Removes the need for manual calculations.</li><li><strong>Accuracy:</strong> Uses consistent baseline noise determination across the chromatogram.</li><li><strong>Validation Support:</strong> Helps confirm method sensitivity in accordance with regulatory guidelines (e.g., ICH Q2, USP).</li></ul><h3><strong>Conclusion</strong></h3><p>Clarity CDS offers a straightforward workflow to calculate signal-to-noise ratio for chromatographic peaks. By first defining the noise baseline and then configuring a custom result column, users can quickly assess analytical sensitivity and peak quality.</p><blockquote><p><strong>For further learning and tutorials, additional videos are available on the </strong><a target="_blank" rel="noopener noreferrer" href="https://www.youtube.com/@DataapexPrague"><strong>official Clarity YouTube channel</strong></a><strong>.</strong></p></blockquote>

How to calculate Signal to Noise ratio in Clarity Chromatography Software

<h3><strong>Introduction</strong></h3><p><strong>User variables in </strong><a target="_blank" rel="noopener noreferrer" href="https://lcms.labrulez.com/products/999"><strong>Clarity Chromatography Software</strong></a><strong> allow analysts to add custom parameters to chromatograms, which can then be applied in tailored calculations and reports. This article explains how to define and manage these variables, where they can be accessed, and how to effectively use them within methods, single analyses, and sequences.</strong></p><h3><strong>Types of User Variables in Clarity</strong></h3><p>Clarity provides <strong>two distinct sets of user variables</strong>:</p><ol><li><strong>Method User Variables</strong><ul><li>Defined within a chromatographic method.</li><li>Apply to all chromatograms measured with that method.</li></ul></li><li><strong>Analysis User Variables</strong><ul><li>Defined for a single analysis or sequence.</li><li>Apply only to specific runs, allowing flexible annotation or parameterization.</li></ul></li></ol><h3><strong>Defining Method User Variables</strong></h3><ol><li>Open the desired <strong>method</strong> in Clarity.</li><li>Navigate to the <strong>Advanced</strong> tab.</li><li>In the <strong>Method User Variables</strong> section, three fields are available to assign names and values.</li><li>Enter the required parameters and save the method.</li><li>These values will now automatically appear in all chromatograms measured with this method.</li></ol><h3><strong>Defining Analysis User Variables</strong></h3><h4><strong>Single Analysis</strong></h4><ol><li>Open the <strong>Single Analysis</strong> dialog.</li><li>Go to the <strong>User Variables</strong> section.</li><li>Enter names and values as needed.</li></ol><h4><strong>Sequence</strong></h4><ol><li>In the <strong>Sequence</strong> window, the variable columns are hidden by default.</li><li>Right-click anywhere in the table and select <strong>Setup Columns</strong>.</li><li>Locate <strong>Analysis User Variables 1–3</strong> in the list.</li><li>Rename them if necessary and move them to the <strong>Shown</strong> section.</li><li>Confirm with <strong>OK</strong>. The variable columns will now be visible and editable directly within the sequence table.</li></ol><h3><strong>Viewing and Editing Variables in a Chromatogram</strong></h3><p>When a chromatogram is acquired with both method-defined and analysis-defined variables, <strong>both sets will be stored together</strong>.</p><p>Within the chromatogram window you can:</p><ul><li><strong>View</strong> the current variables,</li><li><strong>Edit</strong> them if adjustments are needed,</li><li>Apply them in <strong>user column calculations</strong>.</li></ul><h3><strong>Using User Variables in Calculations</strong></h3><p>User variables can be directly included in custom calculation columns, offering the following advantages:</p><ul><li>Adding project-specific metadata to results,</li><li>Storing supplementary parameters directly within chromatograms,</li><li>Automating calculations dependent on user-defined values.</li></ul><p>This capability significantly enhances reporting flexibility and analytical reproducibility.</p><h3><strong>Conclusion</strong></h3><p>User variables in Clarity provide a powerful way to enrich chromatographic data with additional, customizable parameters. By setting them at the method, analysis, or sequence level, analysts can streamline workflows, improve traceability, and adapt calculations to project-specific requirements. Proper use of these variables enables more efficient data management and reporting in chromatography laboratories.</p>

Working with User Variables in Clarity Chromatography Software

<p><strong>When processing chromatographic data, it is common to encounter cases where one or more expected compounds are not detected in the chromatogram. In such situations, their amounts are not calculated, and any formula using these missing values produces invalid results.</strong></p><p>This issue often arises when calculating the total content of a compound group, where not all forms or isomers are always present. A reliable solution is to apply the <strong>IFERROR0</strong> or <strong>IFERROR1</strong> functions, which replace missing values with a defined constant (0 or 1). This ensures calculations remain valid even if compounds are absent.</p><h3><strong>Identifying Missing Compounds</strong></h3><ol><li>Open the result table and change the report type to <strong>“All peaks in calibration.”</strong></li><li>If a compound is missing from the chromatogram, no value will be displayed for that compound.</li></ol><p>Without intervention, these empty results cannot be used in calculations.</p><h3><strong>The Role of IFERROR Functions</strong></h3><ul><li><strong>IFERROR0</strong> replaces missing values with <strong>0</strong>.</li><li><strong>IFERROR1</strong> replaces missing values with <strong>1</strong>.</li></ul><p>This approach is especially useful when summing related compounds—such as isomers—where not all forms are consistently detected.</p><h3><strong>Practical Example: Calculating Total Tocopherols</strong></h3><p>In this example, we want to calculate the total amount of <strong>tocopherols</strong>, which appear in different forms: <strong>α-, β-, and γ-tocopherol.</strong></p><p><strong>Problem:</strong> In the current chromatogram, α-tocopherol is missing, so the calculation of total tocopherols fails.</p><h4><strong>Step-by-Step Procedure</strong></h4><ol><li>In the result table, select the <strong>User Column</strong> used for your calculation.</li><li>Right-click and choose <strong>Edit User Column.</strong></li><li>Apply the <strong>IFERROR0</strong> function to each individual component (α-, β-, and γ-tocopherol).<ul><li>This ensures that if one of the peaks is missing, its value will be treated as zero.</li></ul></li><li>Confirm the changes by clicking <strong>OK.</strong></li></ol><p>Now the total amount of tocopherols is successfully calculated, even though α-tocopherol is absent.</p><h3><strong>Summary</strong></h3><p>By using the <strong>IFERROR0</strong> and <strong>IFERROR1</strong> functions in user columns, you can:</p><ul><li>Prevent invalid results caused by missing peaks.</li><li>Automatically substitute missing compounds with zero or one.</li><li>Ensure robust and reliable calculations of sums or averages across related compounds.</li></ul><p>This method is particularly effective when analyzing compound groups in which not all forms are consistently detected.</p><h3><strong>Conclusion</strong></h3><p>Handling missing values properly is essential for maintaining accuracy in chromatographic analysis. With IFERROR functions, you can ensure that calculations remain valid and meaningful, even under non-ideal conditions.</p><blockquote><p>For additional tutorials and instructional videos, visit the official <a target="_blank" rel="noopener noreferrer" href="https://www.youtube.com/@DataapexPrague"><strong>YouTube</strong></a> channel of the software provider.</p></blockquote>

How to Handle Missing Compounds in Clarity Chromatographic Calculations

<p><strong>Efficient configuration management is essential in analytical laboratories using DataApex </strong><a target="_blank" rel="noopener noreferrer" href="https://lcms.labrulez.com/products/999"><strong>Clarity Chromatography Data System (CDS)</strong></a><strong>. Each operator may prefer a personalized interface layout, tool arrangement, and data display format. This article explains where and how Clarity stores user-specific settings and customizations, including toolbar setups, window positions, and user option preferences. The information is based on an instructional video from the Clarity training series.</strong></p><h4><strong>Understanding User-Specific Settings</strong></h4><p>In Clarity, all user-related interface and configuration data are stored in special files called <strong>desktop files</strong>.</p><p>These files allow each user to maintain a consistent working environment, ensuring that customized layouts and preferences are restored automatically upon login.</p><h4><strong>Storage Location</strong></h4><ul><li><strong>Folder path:</strong> All desktop files are located within the <code>CFG</code> subfolder of the Clarity installation directory.</li><li><strong>File extension:</strong> Each file uses the <code>.dsk</code> extension (short for <i>desktop</i>).</li></ul><h4><strong>Purpose of Desktop Files</strong></h4><p>Desktop files serve as containers for various customization parameters that define how the Clarity interface appears and behaves for a specific user.</p><h4><strong>Elements Stored in Desktop Files</strong></h4><p>The desktop file retains a wide range of user interface configurations, including:</p><h5><strong>Toolbar customization</strong></h5><ul><li>Layout and content of toolbars</li><li>Custom button arrangement and visibility</li></ul><h5><strong>Window sizes and positions</strong></h5><ul><li>Remembered placement and dimensions of all open windows</li><li>Support for multiple monitor configurations</li></ul><h5><strong>Pane layout</strong></h5><ul><li>Arrangement of workspace panes (e.g., chromatogram view, method editor, sequence table)</li></ul><h5><strong>Column width and order</strong></h5><ul><li>Customized width of table columns in various data views</li></ul><h5><strong>Table contents and user-defined columns</strong></h5><ul><li>User-specific data display preferences in tables</li><li>Definitions of custom or user columns</li></ul><h5><strong>User options</strong></h5><ul><li>All parameters defined within the <i>User Options</i> dialog are also stored in the same desktop file</li></ul><p>These settings together define the entire personalized environment for each Clarity user.</p><h3><strong>Managing Desktops for Multiple Users</strong></h3><h4><strong>Viewing the Active Desktop</strong></h4><p>The <strong>name of the active desktop</strong> is displayed in the header of the <i>User Options</i> dialog.<br>This allows the operator to confirm which desktop configuration is currently in use.</p><h4><strong>Assigning Desktops to Users</strong></h4><p>To manage user-to-desktop assignments:</p><ol><li>Open the <strong>User Accounts</strong> dialog from the main Clarity window.</li><li>In each user profile, specify the desktop file to be used.</li></ol><p>By default, Clarity assigns a unique desktop to every user, using a filename identical to the user’s login name.<br>However, this configuration is flexible — administrators can assign <strong>the same desktop file to multiple users</strong>, enabling them to share identical interface layouts.</p><h4><strong>Benefits of Using Desktop Files</strong></h4><ul><li><strong>Consistency:</strong> Ensures that each user’s workspace remains identical across sessions.</li><li><strong>Flexibility:</strong> Supports both individual and shared desktop configurations.</li><li><strong>Efficiency:</strong> Saves time otherwise spent re-arranging windows and toolbars.</li><li><strong>Simplified administration:</strong> Desktop files can be easily copied or backed up for deployment on multiple workstations.</li></ul><h4><strong>Conclusion</strong></h4><p>Clarity’s desktop files provide a robust mechanism for managing <strong>user-specific interface settings and system customization</strong>.<br>Located in the <code>CFG</code> subfolder, these files store everything from toolbar layouts to user-defined columns, ensuring each operator can work efficiently within a familiar environment.<br>Administrators can further streamline workflows by sharing desktops among users who perform similar tasks.</p><p>For additional tutorials and video demonstrations, visit the official <strong>DataApex Clarity YouTube channel</strong>.</p>

Where are the user-related settings stored in Clarity Chromatography Software

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