Adding a project

Projects can be conveniently added and accessed using the Project Wizard. Use this step by step guide to create a new project.

Focus can be launched using various ways. See this page for details. Once launched, you will see Project Wizard of Focus.

Choose Add project from the list in the Project Wizard by clicking it. (If you have already created other projects, you will see them in the list.)

Click Continue or Done, whichever visible.

Project path is a directory which you want to use as the Focus project and is generally on the processing machine and not on your camera computer.

PLEASE DO NOT USE SPACES IN PROJECT PATH!!

In the topmost field, choose a project path by clicking on the black Browse button on the left and selecting a path from the dialog that appear. If you want to create a new folder, you can do so in the dialog.

Now Focus will behave differently if you already have an existing project in the selected path or not.

Focus will identify that a project exist and will add to the list of projects for future reference.

Once you select the project path and is a new project, Focus will give various options for initialisation:

These options are explained below:

• Don't create project: This will cancel creation of project and get back to the Project Wizard
• Initialize from master: This will create new configuration files from the master configurations. You would want to use that if you have first project of this kind.
• Copy from existing project (Shown only in the case you have other projects on disk): This will copy the configuration files from an existing project. You should use this option if in past you had a similar project and want to copy all the configurations and parameters from there. If this options is selected, Focus will ask further to choose a project from the drop down, which should be used as a reference.

Once the project path is properly selected, the Project Wizard already creates required files in the selected files. Few options can be changed at this point:

Project can be named, and can later be used to identify the projects from the list. You can use spaces in the project names.

Project mode defines what kind of project you are working. Focus will show image processing tasks and parameters relevant to the mode. For example, particle picking is available only in Single particle. You cannot run tow modes together. You have following options for mode:

• Drift Correction only: This is ideal for project, where Focus will run along with the data collection, and you want only drift correction during the collection.
• 2D Electron Crystallography: This makes available all the scripts and parameters for 2D Electron crystallography along with the drift correction.
• Single Particle: If along with drift correction, you wish to pick particles and export data to RELION, you should use this mode.
• Electron Tomography: This project mode is for users collecting data in electron tomography. This has special drift correction and export script tailored for electron tomography.

Once you select these options, you can click on Continue to proceed. Then, the Project Wizard will load the main GUI and will open it.