Project and Workspace Management

Projects and Workspaces in cryoSPARC

Projects in cryoSPARC are high level containers corresponding with a project directory on the filesystem, which house all associated Jobs. Each Project in cryoSPARC is entirely contained within a filesystem directory. All the jobs and their respective intermediate and output data created within a Project will be stored within the project directory.

Projects are strict divisions. Files and jobs from different projects are stored in dedicated project directories and jobs cannot be connected from one project to another. A project directory is self-contained, meaning that if you have an intact project directory, you can import that Project into any cryoSPARC instance at any time.

Workspaces on the other hand are logical groupings, like labels, that are created by the user to separate portions of a workflow for ease. A job can be added or removed from multiple workspaces. Workspaces do not have any particular directory on the filesystem.

When to create a new Project

Recommendation: Create a new Project for each new unrelated sample on which you are collecting data.

Additional recommendations for creating new Projects and Workspaces:

• Collecting new data for the first time on a new target molecule: Create a new Project and a new Workspace within it. Import the movies/micrographs/particle stacks into the new Workspace.

• Collecting data a second or subsequent time on the same sample/target (potentially the same or different grid from the same batch, potentially on a different day): Use the existing Project and existing Workspace where you processed the first set of images. Import the movies/micrographs/particle stack into the existing Workspace or a new Workspace, in the same Project.

• Collecting data on a new sample/grid/preparation of the same target molecule: Use the existing Project, but create a new Workspace. This allows easy re-use of 3D volumes, 2D templates, and easy combining of particle images downstream. You can create multiple Workspaces within a Project, for example if collecting/processing new data from a similar sample.

See similar considerations for creating Projects and Sessions for cryoSPARC Live in the New Live Session: Start to Finish Guide

Creating your first Project

1.Navigate to the Projects view by clicking on the drawer icon on the header, or from the Projects button in the footer. ​​

2. To create a project, press N or click on "+ Add" on the header, which will bring up a modal window for the New Project details. ​​

3. Enter a project Title and select a location for the associated project directory from the File Browser. The project directory you select should already exist, and it will be populated with job directories as you create jobs. All files associated with the project will be stored inside the selected project directory. You may also wish to enter a Description for your project.

4. Your new project now appears on the Projects page. ​​

5. To open the Project, click on the "Px" button on the top left hand side of a Project card:

6. You can view Project details and actions from the Project Details panel:

Creating your first Workspace

Before you can start processing data inside of a new project, you will need to create at least one workspace.

1. Click the project number (e.g., P44) to open the Project within which you want to create a Workspace.

2. Once inside your selected Project, create a New Workspace using the "+ Add" button on the header or N on your keyboard. Or, you can click New Workspace from the Project Details panel on the right. Workspace titles can be changed later, and descriptions can be added any time.

3. You can open a Workspace either by clicking on the Px - Wx button for a particular Workspace (pictured immediately above), or you can locate it using the Workspace search bar in the header.

4. You can enter notes or details about the Workspace and find available actions from the Workspace Details panel:

Once you have created at least one Workspace within a Project, you can start creating jobs:

pageCreate and Build Jobs

Additional Project and Workspace Actions

Share a Project

Only users who own a particular Project or have a Project shared with them can see Workspaces, cryoSPARC Live Sessions and jobs within those Projects. To add a user to a Project, navigate to the Project Details Panel for a particular project (owner should be the logged in user) and click Share With Users to select the user you wish to give access.

Delete a Project

Navigate to the Workspace and locate the 'Delete' button on the Workspace Details Tab. A pop-up message will ask you to confirm the delete. Once you confirm, another popup will show you a list of jobs and workspaces that will also be deleted and ask you to confirm again. Deleted jobs are first cleared before deleting, meaning that their intermediate and final results are erased from disk. Note that unlike deleting jobs, deleting a project doesn't remove the project folder from the disk.

Delete a Workspace

Navigate to the Workspace and locate the 'Delete' button on the Workspace Details Tab. A pop-up message will ask you to confirm the delete. Once you confirm, another popup will show you two lists: A. jobs that reside only inside the selected workspace, and that will be fully deleted, and B. jobs that exist in the selected workspaces, and other workspaces (i.e., because they were linked). Jobs that exist in multiple workspaces (list B) will not be fully deleted. They will simply be disassociated from the workspace to be deleted. Note that deleted jobs are first cleared before deleting, meaning that their intermediate and final results are erased from disk.