Inspecting Job Data

Selecting Jobs

The sidebar automatically displays information pertaining to the selected jobs. Click to select a job, use the arrow keys to navigate between jobs, and press command +click to add or remove jobs from your selection.

Job Info Tags

Almost all jobs include summary information presented on the cards, table, and tree view - these are called info tags. For example, the Blob Picker job card now displays key information in tags anchored around the preview images to display the minimum and maximum diameter configured, how many micrographs were processed, how many particles were picked, and the average number of particles picked per micrograph:

The combination of job preview images, info tags, and additional metadata displayed on the job card footer makes it easier to distinguish between multiple runs of the same job type with different parameters and results.

Job Dialog

You can inspect a job to view much more information about it, including an interactive dashboard, real-time log of events, and interactive utilities. To inspect a job, select it and press spacebar or click on the ‘View Job’ button from the sidebar or click on the job ID and type on the header of the job card.

The job preview dialog opens above the current page and can be dismissed at any time by pressing the spacebar or escape key or clicking on the ‘x’ button.

At the top of the job inspection dialog is a breadcrumbs element depicting the hierarchy of a job. Clicking on a project or workspace will navigate to that page. Clicking on the job will navigate to the workspace page and scroll to that job.

Alongside the breadcrumbs, you can star the job and view the elapsed time.

The bottom of the dialog contains a footer with helpful information such as what processing node the job was queued on, how many GPUs were allocated and what custom parameters were set:

The job inspection dialog is comprised of various tabs that provide more detail into the processing history and results of the job. To the right of the dialog’s main content area is a collapsible sidebar that lists all output groups the job produces. From this sidebar you can drag and drop output groups into the job builder or download results.

Close the sidebar (top-right button or command + /) to expand the visible area of the job inspection dialog.

Dashboard

The job dashboard is a new view introduced in CryoSPARC v5.0. It is the default tab when opening the job dialog and includes a concise overview of key job stats, errors and warnings, all chart images created by the job sorted by general relevance, and a collapsable panel which shows the most recent text events output by the job.

Info Cards

Info cards are located at the top of the panel. They include all of the data available in the info tags that appear on the job card as well as as some extended information. Values in the info cards can be clicked to copy to the clipboard.

Errors and Warnings

Errors and warnings are embedded directly into the dashboard and organized together to quickly surface this information.

Errors/warnings populate the module in descending order and can be copied to the clipboard by clicking the “copy” button in the top right corner of the message (becomes visible when hovering the message).

Charts

The charts section contains all of the chart images that have been output by the job. These are the same images available in the job’s event log, ordered by relevance, and set to the most recent iteration by default.

Expanding and Collapsing Charts

Charts exist in collapsable sections that correspond to their “chart type” (eg. Real Space Slices, 2D Classes, etc). Charts are sorted by general relevance with the least relevant charts sorted to the bottom and collapsed by default. The expanded/collapsed state for charts can be controlled in a few ways:

A chart can be expanded or collapsed by clicking on its individual section header.
All charts can be expanded at once by clicking the “Expand All Charts” toggle button (arrows pointing away from a dotted line) on the Charts section header.
All charts can be collapsed at once by using the “Collapse All Charts” toggle button (arrows pointing towards a dotted line) on the Charts section header. This can be helpful when trying to find a specific chart type in a job that outputs many charts.
Charts can be reset to their default expanded/collapsed state by using the “Reset” button on the Charts section header.
All charts can also be expanded or collapsed by holding down the command key and clicking the header of an individual chart type.

Iterating Charts

Charts are set to the most recent iteration available by default (if applicable, for jobs that output multiple iterations of the same chart type as they progress). By moving the slider, iterations can be scanned to see how the job progressed or is currently progressing. There are two iteration sliders available in the view:

The global iteration slider is available on the Charts section header. This slider will progress through all available iterations across all charts.
- Many charts do not output new images on each iteration as the changes are not significant enough to warrant it. If a chart does not have an image for the iteration specified in the global slider, it will continue to display the chart image for the last available iteration and will show a small orange “unlinked” icon in its header to indicate that the chart image iteration does not match the slider’s current iteration.
The local iteration slider is available in the header of a specific chart. This slider controls the iteration for that chart only.

The chart lightbox allows a chart image to be expanded to its full size and viewed in isolation.

Open the lightbox by simply clicking on any chart image on the dashboard. The lightbox can be closed by clicking outside of the main area on the darkened backdrop, clicking the red “X” button in the top right corner of the content area, or pressing the escape key.

The lightbox includes a number of features to help you navigate between chart images quickly and efficiently:

The Chart Type Switcher is the second button group on the left side of the header. It has a central button which displays the chart type (eg. Real Space Slices, FSC, etc). This button opens a menu containing all chart types the job generates, allowing you to switch the lightbox to any chart type you wish to view. The arrow keys on either side will iterate incrementally through all available chart types. Both of these actions will reset the iteration and index between chart types.
- Chart types can also be switched between by holding down the command key and pressing either the leftarrow or rightarrow keys to navigate.
The Chart Switcher is located in the bottom left corner of the lightbox. It includes navigation arrows to iterate between charts, an input to manually set the chart index, and a button that indicates the number of total charts available for the chart type (clicking this button selects and switches to the final chart of that type).
- Charts can be also be switched between by pressing either the leftarrow or rightarrow keys to navigate.

The chart’s iteration can be controlled using the slider located on the right side of the lightbox header (if applicable). This slider operates the same way as the local iteration slider, and will update the current iteration for the specific chart being viewed.

The lightbox also includes a click to copy title for the current job image directly below the header, and a click to copy timestamp representing when the chart was created by the job in the bottom left corner of the footer.

The download module in the centre of the footer includes buttons that can be clicked to download any of the available file types for the current chart. In the case where a chart type contains multiple iterations, a GIF download option is presented.

Interactive Charts

Interactive event charts are embedded directly into the job dashboard if they are available. These charts allow for deeper exploration of generated output data through rich interactive features.

Interactive charts are contained in a collapsable "Interactive" section module. Each chart is contained in its own named section which can also be collapsed.

Above the chart is a control bar where all relevant filters and chart settings are shown. Below the chart is a footer which includes timing information and a module to download event data files (eg. a png of the event image).

Interactive charts are currently only available for 3D Variability Display jobs

Embedded Event Log

The job dashboard includes an expandable text only event log attached to the bottom of the panel. This event log includes the 120 most recent text events (including errors and warnings) and tails the log, always showing the most recent events as they appear from the bottom.

The event log is pinned to the dashboard footer and will always be visible when scrolling. The event log panel can be expanded or collapsed by clicking the +/- toggle button. Its height can also be adjusted by grabbing the top edge of the header (which will become highlighted blue) and then dragging it to the desired height.

The event log also includes a button group in its header to download relevant logs. The lefthand button downloads a pdf of the entire event log, while the righthand button opens a menu with the option to download the full job report.

Event Log

As a job runs, events are published in real-time as a job processes. Events are viewable when a job completes. Above the log, a list of controls are available:

Show from top: Jump to the top of the event log, scroll to load events in chronological order.
Follow latest: Skip to the last available checkpoint and listen for new events.
Select a checkpoint: View a list of checkpoints and timestamps, click to jump to the start of the checkpoint.
Filter types: Display events of a certain type (such as text or image).
Filter flags: Display events of a certain job-dependent flag (such as central slices or FSC curves).
Show CPU usage: Display CPU memory usage of the processing node alongside each log.
Show timestamps: Display a timestamp alongside each log (you can also hover over the icon on the left side of each log to view the timestamp).

Interactive

The interactive tab is only visible when running an interactive job that is in ‘waiting’ status. Please refer to the Interactive Jobs guide to learn more.

Inputs and Parameters

In addition to the details sidebar, this tab displays all inputs and parameters that were configured. Select 'Show slots' to view low-level slots contained within each input group. Parameters will be marked as either default (grey/blue) or custom (green). Advanced parameters are denoted with an ‘A’. You can toggle between listing only custom parameters or all parameters.

Outputs

In addition to the output groups sidebar panel, the outputs tab displays a comprehensive overview of all the output groups and individual outputs a job creates. Please refer to the Job Builder Tutorial to learn more about how you can take advantage of the low-level results CryoSPARC generates.

Volumes

This tab is only visible when a job outputs one or more volumes. By selecting a volume from the left sidebar, it will load in the integrated volume viewer. You can set a threshold, zoom and pan, start or pause animation, and download the volume for inspection in an external software.

For volumes that also have an associated colour map (such as running a refined volume through Local Resolution Estimation), an additional option will become available in the sidebar to view the coloured volume.

Metadata

Useful for when archiving or debugging, the metadata tab contains all job data stored in the database. You can search for specific fields using the search bar. The path to the job logs location on disk is listed as well and can be clicked to copy.

In addition to the job data, you can view the text log of the job by clicking on the ‘Log’ sub-tab:

When a job is selected or inspected, the sidebar details panel will list an overview of what other jobs are connected to it via parent or children connections, or it being cloned from another job of the same type. Hovering over each job will display a tooltip containing an outline of that job, including what parameters it has been configured with. Clicking on a related job will inspect it. To open the related job in a new tab, click it while pressing the command (macOS) or control (Windows, Linux) key.

Comparing Jobs

The comparison view is designed to enable analysis of multiple jobs side by side to compare and contrast their settings and results. It includes the ability to view differing parameters aligned between jobs, inspect job chart output images to observe how job progression has diverged during processing, and the ability to download outputs from multiple jobs in a single click.

Opening the Comparison View

The comparison view can be opened by selecting multiple jobs (command + click ) and then either clicking the “Compare” button at the bottom of the multi-select sidebar, or simply pressing the spacebar.

Header

The header includes all essential identifying information for each job, and is pinned to the top of the dialog to keep it visible while scrolling down to different sections.

This section contains the job’s unique ID, its job type, a button to star the job, and the job’s title (if applicable):

The job ID has a dual function as a button that can be clicked to navigate to that specific job’s dialog. Using the web browser’s “back” button will navigate back to the comparison view.
The star button allows the job to be starred directly from the comparison view, it will turn yellow when the job is starred.
The job title field will be automatically shown if any job in the comparison has a title, and hidden if no jobs in the comparison have a title. The field can be manually shown or hidden by clicking the toggle button on the far right side of the Summary section header below the title. Clicking the title will convert it into an editable field, clicking away from it will save the title and switch out of the editing mode.

Summary

The summary section includes the job’s cover image, info tags, and description.

Located on the far right of the summary section header are toggle buttons to show/hide the title and/or description as well as a button to download all relevant outputs from each job in the view.

The Download Job Outputs button opens a sub-menu where the type of outputs that you would like to download can be checked or unchecked to add them to the download. The download can be made as individual files which will be downloaded sequentially, or a single zip. We recommend using the individual option generally, as the zip option can consume a significant amount of memory for large files, which can cause the browser to lock up or crash in some cases.
The job description field will be automatically shown if any job in the comparison has a description, and hidden if no jobs in the comparison have a description. The field can be manually shown or hidden by clicking the toggle button on the far right side of the Summary section header. Clicking the description will convert it into an editor, and clicking the red “X” button in the top right corner of the editor will switch out of editing mode.

Parameters

The parameters section allows for comparing and contrasting the differing parameters between jobs in the comparison view. The default setting is to show all parameters that are different between jobs (where at least one job has a custom value for that parameter) and to show all advanced parameters.

Each parameter is sorted and aligned in a grid with rows that stretch across all job columns. Custom parameters are shown in green with a corresponding “C” icon. An “A” icon is displayed if the parameter is advanced, and a “D” icon will be shown if it has a default value.

The Parameters header includes a button group where each button is a toggle used to hide or show sections for different, custom, and/or default parameters. A separate toggle button for “advanced” controls whether advanced parameters are shown or hidden across all parameter sections.