Browsing the CryoSPARC Instance
Last updated
Last updated
In order to interact with CryoSPARC and process data, you will need to browse the instance, navigating through the various projects, workspaces, sessions, and jobs that you and other users in the instance create. The Browse System is a set of tools and interfaces that help move around the instance and find the items you are looking for.
The browse system contains five fundamental components:
Browse Header: The header sits above the main working area and provides options for high level navigation and creation.
Control Bar: The control bar is where all actions involved in filtering, sorting, or setting a view option reside.
Content Area: The main space in the browse system is the content area. This is where projects, workspaces, sessions, and jobs are shown in either card, table, or tree view.
Footer: The footer shows total counts, curated filter options, and can be toggled using the footer switch button on the far left of the bar to show general active job and target information.
Sidebar: The sidebar shows contextual information and applicable actions for any selected items.
From the CryoSPARC dashboard, browsing the instance begins with clicking on the container icon in the left-side navigation bar. This button brings you to the project cards view, showing all projects you have access to across the instance.
When browsing through projects, workspaces, sessions, and jobs, each item will be displayed as a card by default.
Projects, workspaces, and sessions have buttons at the bottom of the card which can be clicked to open that item and navigate into a view of its contents. Jobs cards can be opened by clicking on the actionable header button which will expand the job inspection dialog.
Each type of card can also be selected by clicking on it, which will highlight it in blue and populate the sidebar with its information. From here the item can also be entered by clicking the “View” button at the bottom of the sidebar, or by pressing the enter key on your keyboard for projects, workspaces, and sessions, or the spacebar for jobs.
The quick switchers at the top left of the page indicate your current location within the instance, and allow for quickly entering, exiting, and switching between projects, workspaces, and sessions. The solid blue switcher indicates the type of items you are currently looking at in the main content area.
These switchers can be used to quickly jump around the instance by clicking the arrow button on the righthand side of the switcher to open the selection dropdown.
Once you navigate inside a project, workspace or session, an “X” button will appear on the lefthand side of the corresponding switcher. Clicking the “X” button will deselect the option and navigate you back up one level of navigation, while clicking the name will reopen the selection menu and allow the quick selection of a different option.
The Quick Access Menu is available by clicking on the menu icon in the bottom left corner of the page.
The menu is composed of three tabs: Recent, Starred, and Tags. Use these menus to quickly jump to important items in your instance.
Recent: recently accessed items. Clicking on a project or workspace will open it and navigate you into the relevant section of the browse system. Clicking a session will navigate you into that session in the CryoSPARC Live view. Clicking a job will open its dialog without navigating away from your current location.
Starred: items that you have starred. Starring items can be done directly from the items card’s header, and for jobs can be done in the header section of their dialog as well.
Tags: all of the available tags across the instance along with counts of how many items they have been applied to. Clicking items will send you to a browse view with the selected tag applied as a filter. This quick access menu tab is covered in more depth in the “Tags” section below.
The last menu tab you accessed is remembered by the browser in the current browser tab until closed. This is in order to aid in navigating swiftly between items even when closing and reopening the menu. Each sub section inside of each menu tab is a drawer that can be closed by clicking the section header (e.g., Recent Projects). When an item is closed it will remain closed between browser tabs and even if the browser is closed and reopened. This allows you to organize each tab of the quick access menu to only show the items that are most important to you.
The spotlight allows unrestricted navigation through the interface and can be opened by clicking the magnifying glass icon in the navigation bar, the search bar button on the home page header, or by pressing the command + k keys together on the keyboard.
The spotlight input is automatically focused and you can begin typing into it immediately. Many commands are available, such as creating a new item, opening the jobs builder, or attaching a project.
Commands specifically for navigation include viewing all items in a granularity, or typing in the name of a project, workspace, or session to quickly find and open them.
When browsing the CryoSPARC instance, you can select a view from the buttons in the top right corner of the content area.
Items in CryoSPARC display as cards by default. Each card includes a header with the ID and title of the item along with action buttons for opening the card’s action menu and starring the item.
The card can be selected by clicking on it anywhere that is not an actionable button. This will add a blue selection outline to the card and add all of its relevant information to the sidebar. Once selected, the item can be opened by pressing the enter button on your keyboard (for projects, workspaces, and sessions). Items can also be opened by clicking the “view” button(s) at the bottom of their respective card, or by clicking the view button at the bottom of the active sidebar. Entering the selected item will navigate into the item and show all of its contained items (eg. entering a project will navigate to the workspaces view and show all of the workspaces belonging to that project). For jobs, selected cards can be opened by pressing the spacebar to expand the corresponding job dialog. Job cards can also be opened by clicking the card header button with the job ID and name.
The table view organizes each item as a row in a table. This can be particularly useful for getting an overview of large numbers of items and for accounting purposes. When the row is selected it will highlight blue and can be opened the same way as with a card, by pressing the enter button on your keyboard or by clicking the view button at the bottom of the sidebar. The download button at the bottom right of the jobs footer allows for exporting the entire data selection with the same filter, sorting, and granularity options as the table view in a CSV file.
The tree view is a unique view only available for jobs inside of a workspace or project. This view lays out all jobs as an interconnected network branching out from the first job(s) in the processing pipeline. Each job is linked to previous and subsequent jobs by coloured lines representing the flow of inputs and outputs between jobs.
Navigate the tree view using the two control palettes present in the bottom left and right corners of the viewing area. Zooming is the default scroll-wheel behaviour, which can be changed by clicking the “pan” icon in the bottom right corner of the tree view. Default zoom levels are shown in the bottom left corner of the viewing area. These can be used to quickly toggle between different levels of zoom to quickly move the entire view in or out to a set scale factor. When first switching to the tree view, all trees will be centred within the view both vertically and horizontally, making it easy to locate your data immediately upon entry.
Tree view job cards contain a more condensed version of the job data available in the standard cards view. Available actions are shown on hover in a command palette located in the bottom righthand corner of each card. Right clicking the card will show the quick actions menu just like cards from the card view and rows in the table view. Additional information is shown in a tooltip that will appear above the card when it is hovered for a short period of time. These tooltips along with the quick actions menu make it easier to see relevant job details and act on the job without needing to change your zoom level in order to do so.
Due to the unique structure of the tree view, sorting actions cannot be applied in this view.
