UI Overview
CryoSPARC Live UI Overview
From this page, you can view details of existing Sessions including current processing status and create new Sessions. The Browse Sessions page contains four components:
- 1.The header contains the main menu, toggle between the browse view and data management view, and button to create a new session
- 2.The projects list on the left side of the screen shows a list of all projects that contain Live sessions
- 3.The session list is shown in the middle of the screen and shows a card for each session. Clicking on a session will show more information in the sidebar
- 4.The sidebar on the right side of the screen populates with detailed information of the selected session
There are many options available to filter sessions, such as selecting a status, what project it belongs to, and who created the session.
To open an existing session, click ‘View Session’. To create a new session, please see: 1. Create New Session
CryoSPARC Live User Interface
The Header contains information about the session status, session and project title, as well as session-level functions (Start, Pause, Mark as Complete, etc) and the elapsed time. The Main Menu on the top left contains options for navigating back to the Browse Sessions page, as well as session settings and logout.
The Sidebar is the main way to navigate through a Live session from start to finish and also contains detailed statistics for each processing stage, e.g., the number of exposures found and processed, the number of particles extracted, etc. Click on a sidebar item to navigate to the corresponding tab. Sidebar items can be collapsed or expanded.
You can collapse various tabs to show or hide certain statistics
As exposures are captured, detected, and loaded into CryoSPARC Live, a visualization/thumbnail for each appears sequentially from left to right in the top bar. Near the bottom of each thumbnail, a blue progress bar indicates the status of pre-processing (motion correction, CTF estimation, picking, extraction, etc). Rejected exposures are indicated with a red “X”.
The arrows allow for traversing through exposures including the ability to follow the latest exposure, or navigate to a specific exposure using its ID.
Each tab allows for configuration or inspection of a data processing stage. The Configuration tab contains session information, notes, hardware selections and parameters, with the option to trigger re-processing of previously processed data if parameters are changed. The Picking tab contains the ability to choose between the three available pickers, set, test and apply parameters and thresholds. More details can be found in: How to Start to Finish.
The selected exposure (highlighted with a green border in the Exposure Feed) is expanded in the Exposure / Volume Viewer, allowing zooming/panning and filtering of the micrograph, display of motion trajectories, and CTF plots/Thon ring diagrams associated with the exposure. Particle picks associated with the exposure are shown (colours correspond to the different picking tools available in cryoSPARC Live) and manual picking can be done directly on the micrograph.
Once a 3D Volume is available (following Ab-Initio Reconstruction or Streaming 3D Refinement), the volume can be examined in the same viewer. You can set a custom threshold value using the slider or input on the top-right of the viewer. You can also download the currently displayed volume using the button on the bottom-right of the viewer. There are several controls available to manipulate the volume: zoom by using the scroll wheel on a mouse or trackpad, rotate via holding the left mouse button and dragging across the canvas, pan via holding the right mouse button and dragging across the canvas. You can pause or play the rotation animation via the button on the bottom-right of the viewer.
The ruler and scale bar allow for easy size reference of an exposure and particles. The scale bar appears in the top right of the exposure viewer and shows a size reference in nanometers relative to the current zoom level of the exposure. It reactively scales while zooming and will change colour to maintain contrast over the exposure. The ruler tool can be selected in the exposure controls menu on the bottom right of the exposure viewer. When clicking and dragging on the exposure with this tool selected, a circle will be drawn emanating from the initially selected point with both its diameter in pixels and angstroms relative to the current scale displayed.
The Footer contains information and links to active Live session jobs. Clicking on a job will open its event log via the Live interface.
There are nine tabs within a CryoSPARC Live session that contain all the controls needed, from configuration to inspecting and filtering exposures, particles and 2D classes and attaining 3D reconstructions from selected particles. The currently selected tab is highlighted in blue and displays an arrow to the right.
To view a particular tab, simply click on the name within the navigation sidebar. Underneath the title of each tab are statistics computed by CryoSPARC such as the number of processed exposures, particles extracted and selected for classification, and results of the reconstruction stages. You can choose to show or hide the statistics of each tab by clicking on the expand or collapse button at the right of each tab. Choose to hide or show all details by holding shift and clicking the toggle button for any tab.
The details tab shows a high-level overview of the session including a complete processing history. Various actions are available, including the ability to export exposures or particles. You can also provide notes for the session, which is particularly helpful when looking back at a later date.
The configuration tab automatically loads when a session is first created, but you can navigate back to it at any time. It contains three panels:
- 1.The first panel shows an overview of the compute resources selected to run the session. Live runs on the same processing lanes configured for CryoSPARC. You can select what compute resources to use for preprocessing and reconstruction stage, along with any auxiliary processing that Live performs. It's possible to adjust the number of GPU workers allocated for the preprocessing stage throughout the lifecycle of the session. For example, at the start of the session, you can allocate four GPUs to quickly extract particles from exposures, then lower the number of workers to two or one when resources are needed for the reconstruction stage
- 2.The second panel contains all parameters available to configure. There are a few required parameters that must be provided before a session can start, such as the microscope and camera details. You can view advanced parameters via a toggle and use the text input to quickly filter through the list. Once you change one or more parameters, you have the chance to apply the changes to all exposures in the session or only future exposures. This is helpful when deciding to change parameters while the session is currently processing exposures. Upon clicking apply, Live will automatically determine the best way to reprocess exposures based on the new configuration
- 3.The third panel within the configuration tab is used to configure exposure groups. Exposure groups specify where to find files that you'd like to process. You can provide additional options such as a gain reference file for each exposure group. Multiple exposure groups can be added in a session, and they can be used for a variety of purposes. For example, you can choose to configure one exposure group per grid, or an exposure group for each beam-shift position in a template. After enabling an exposure group, you can choose to continuously listen to the specified directory and filename wildcard filter for new exposures, or ignore the group if you no longer want to include a set of exposures for processing.
To speed up the configuration a new Live session, you can save all or some of the parameters of an existing session into a configuration profile. These profiles are available for all users to apply to current or future sessions. To save your current configuration, click on the 'Profiles' button at the top of the first panel. The profile section that appears in the first panel is also where you can view and apply existing profiles to the current session.
The individual tab contains details of the currently selected exposure, including diagnostic plots on the left side of the screen, and an interactive exposure viewer on the right, complete with a manual particle picker and particle inspection controls for manual, blob and template picks.
Under the individual tab button within the sidebar, properties that are common across all exposures within the session are displayed including the exposure dimensions, pixel size and number of frames.
By default, the selected exposure is the most recent exposure that has been fully processed. You can use the exposure feed to scroll across all of the exposures within the session and click to select one. You can also right click an exposure to view even more details about it. Additionally, you can use the exposure navigation controls in the header to navigate to the latest available exposure, first exposure, and anywhere in between. When set to show the latest exposure, the interface will automatically load and display new data as it becomes available.
Hovering over the exposure viewer will display a set of controls such as changing the zoom level and setting the lowpass filter value.
Additional details regarding the selected exposure are shown above the exposure viewer, including the status of the exposure and what exposure group it is contained in. Clicking on the exposure details will reveal further options, such as the ability to reject it from further processing, option to reprocess it, or view and copy the path of the exposure.
To the right of the exposure details are the exposure pick details. Each type of pick is shown as a different colour: manual picks in green, blob picks in yellow and template picks in red.
The display of each picker type on the exposure viewer can be toggled by clicking on the corresponding picker type button. The number of picks shown on the selected exposure is listed first, and if particles have been extracted, the number of extracted particles from the selected exposure is shown to the right of the arrow. More picking statistics and display options are available by clicking on the picking menu dropdown. Each type of pick can be displayed as a point, circular outline of the particle diameter, or extraction box size.
The overview tab is a powerful view in cryoSPARC Live that allows for inspection of 20 different attributes across all exposures in the session. Exposure-level details such as time of processing, motion statistics, CTF fit, relative ice thickness and picking statistics are shown as scatter plots, with new exposures automatically added when they are processed. When you hover over a point in any plot, a preview of the exposure will display on the left side of the exposure viewer. Clicking on a point in any plot will select it and show it in the exposure viewer.
At any time while a session is running, you can choose to set session-level thresholds based on any attribute value using the input boxes, slider or dragging a vertical region on the plot. Once confirmed, all current and future exposures that are contained within the range of the threshold will be noted as accepted. Exposures outside the threshold range will be marked as rejected and excluded from further processing. Exposures that are marked as accepted will be displayed in blue and rejected exposures are displayed in red.
Thresholds are applied in an additive manner, and can be cleared at any time. Applying thresholds is a great way to filter exposures based on their quality. For example, you may choose to exclude any exposure that has a calculated CTF Fit (Å) value greater than 4 angstroms.
Under the overview tab button within the sidebar, any attribute with a threshold applied will display with the set minimum and maximum value.
The browse tab is another great tool for exploring exposure data across the session. A scatter plot with a configurable X and Y axis is displayed on the top-half of the tab, and table of all exposures processed is displayed on the bottom-half of the tab. Just as the overview tab, accepted exposures are shown in blue and rejected in red and any exposure can be selected by clicking on a point. Hovering over a point will reveal a preview of that exposure on the left side of the exposure viewer. The dropdown menu can be used to filter the exposure table, and the download button can be used to save exposures shown in the table as a CSV file, which respects the applied filters and sort options at time of download.
The picking tab contains all the controls needed to activate and filter either manual, blob or template picks. By default, the blob picker is activated at the start of every session. The active picker is always displayed in the sidebar under the details tab button. To view options for another picker type, click on corresponding button at the top of the tab.
The manual picks table will automatically update when new manual picks are added. To add or remove manual picks, hover over the exposure viewer and select the add or remove actions at the bottom right. When the 'add' picks mode is active, left click to add a pick and right click to remove a pick. When the 'remove' picks mode is active, left click to remove a pick.
To extract manual picks, click the 'Start Manual Extraction' button at the bottom of the tab.
If there are any manually picked particles in the session, the total number of picks and number of exposures with manual picks will be displayed under the picking tab button within the sidebar.
Within the blob picking section, you have the ability to adjust any blob picker parameters and apply that to all exposures or any future exposures. Additionally, you can 'test' a single exposure with different parameters to see the result in the exposure viewer before committing to applying those parameters. Test exposures will display in the feed with a the letter 'T' in a purple tag, and any test exposures can be reset via the exposure menu.
Blob picks can be filtered in the section below, allowing you to adjust the NCC and power thresholds and confirm those thresholds. Once confirmed, you can choose to extract particles using the new thresholds for all or only future exposures. As you adjust the thresholds, helpful messages will appear below stating an estimate of how many picks will remain if the new thresholds are set. Additionally, a description of what picker is currently active and using what settings will also be displayed below the thresholds.
The template picker can be activated by creating or loading templates for the template picker to use. You can generate templates using existing manual, blob or template picks from the current session or load existing templates from another CryoSPARC job. Additionally, you can load templates from a completed streaming 2D classification job within the session if one has completed.
Once templates are loaded, you can select one or more templates for the template picker to use. The template picking tab also contains similar sections to adjust parameters and filter and extract template picks as displayed in the blob picker. The template picker can be activated when at least one template is selected for the picker to use and all parameters are configured.
Under the picking tab button within the sidebar, blob or template picking details such as the extraction box size and picking diameter will be shown for the active picker.
The 2D classification tab allows for the classification of particles extracted within the session. Once you are happy with the number of picks available in the session, a classification job can be started. Within CryoSPARC Live, 2D classification operates in a steaming fashion and will automatically classify new particles as they become available. At any time, you can restart the classification job or choose to start a new job and configure custom parameters via the CryoSPARC interface by using the purple build button.
The interface will automatically update to an interactive mode when 2D classes are ready for selection. All particles within selected classes will continue to the reconstruction stage.
Under the 2D classification tab button within the sidebar, details regarding classes and particles are shown, along with progress messages that update in real-time. Within the sidebar or at the top of the tab, you can click on the project and job ID of the streaming 2D classification job to view detailed logs and diagnostic plots for the job. Click on the close button at the top right of the screen or press spacebar to return to the main interface.
The ab-initio tab allows you to configure and view an ab-initio model to be used for the refinement stage. You can either load an existing volume from a CryoSPARC job within the current project or run an ab-initio job based on particles from the session. An ab-initio job can be run once at least one 2D class is selected. Once in progress, based on the number of classes, one or more volumes will appear in the tab. Each volume can be selected and its 3D preview will update in real time as the job progresses.
Similarly to the 2D classification tab, details of the ab-initio job will be displayed in the navigation sidebar. You can inspect the log output of the job by clicking on the job identifier within the sidebar or at the top of the tab.
The final tab and last stage of Live processing is the refinement tab, which will run a homogeneous refinement on all selected particles in the session. You can configure a refinement job by ensuring an ab-initio volume has been loaded into the session and specifying a symmetry value. Additionally, you can choose to configure custom refinement parameters via the CryoSPARC interface using the purple build icon. Within CryoSPARC Live, the refinement operates in a steaming fashion and will automatically update when new particles become available.
Once a refinement job has started to process, its volume will automatically load and continue to update as the job progresses. Diagnostic plots will appear and update over time.
You can use the volume viewer to interact with the map, adjust the contour threshold, and download the map.
Similarly to the ab-initio tab, details of the streaming refinement job will be displayed in the navigation sidebar. You can inspect the log output of the job by clicking on the job identifier within the sidebar or at the top of the tab.