Particle

Create a Project Space

Access: CP::MenuBar::Project and CP::DataView

Create a New Project Space

In PARTICLE, when starting a new data analysis project, the first step is to create a "project space", in which the program will manage the data, procedures and results with an internal file structure. To create a new project space, go to MenuBar::Project::New, which opens a file browser prompting for a location and name of the project. A project space contains the following standard folders (a.k.a. directories):

Folder	Contents
micrograph	Electron micrograph data (MRC format with the extension "mrc").
screening	Templates for computational screening and CMX files.
particles	Particle coordinates and particle stack from each micrograph, and the full stack for classification & reconstruction.
alignment	Alignment references, aligned stacks and CMX files.
classes	Particle classes and CMX files.
modeling	Reconstructed 3D density maps and CMX files.
scripting	Procedural scripts generated from Visual Scripting.

Import Data to the Project Space

After a project space has been created, move (or link, or copy) all raw images to the "micrograph/" folder so that they become "visible" to PARTICLE. All image data should be in the MRC format with the extension "mrc" (lower case). From now on, the user should access the data exclusively through the program GUI. Note that the data is not imported into the project space yet until the image filenames appear in the spreadsheet of DataView.

To import multiple micrographs at once, activate CP::Menu::Project::Data::Import, which opens an editor (replacing CP::Monitor at the upper-right region of CP) to display all recognized image files in the "micrograph/" folder. After making proper changes to the list (e.g., removing unintended images or those already in the project space), activate the Import Data to Project Space button on top of the editor to add all the images in the list to the spreadsheet. These images are now entered into the project space and will be managed by the program. A single micrograph can also be imported to the project space via the button DataView::+ below the spreadsheet.

To remove multiple micrographs from the project space, inactivate the selection flag (set Act to empty, see the table below) of those entries, then delete them via CP::Menu::Project::Data::Delete. A single micrograph can also be removed from the project space (mouse LeftClick to highlight in the spreadsheet) via the button DataView::–.

The import and delete functions can be applied repeatedly in any order when setting up a project space.

Image Property Display & Editing

In the DataView spreadsheet, each row corresponds to one micrograph entry and contains a summary of the following key information:

Column	Attribute
Act.	Data selection flag. : the micrograph is selected (i.e. active); : the micrograph is not selected (inactive); Click the label to toggle the status. Once activated, both the image and its corresponding particle stack will be included in the data analysis and batch processing.
Micrograph	Micrograph file name. The file path and extension are omitted for simplicity.
Pix. Size (A)	Pixel-size of the digitized image (in Angstroms).
Particles	Number of particles annotated in the micrograph.
Defocus (um)	The defocus value and astigmatism of image CTF. For image with astigmatic defocus, the defocus value is (defocus_x + defocus_y) / 2 and the astigmatism value (in parenthesis) is \|defocus_x - defocus_y\| / 2
Group ID	Group name of a micrograph (for tilt-pair & tilt-series). Single-image: the micrograph file name itself; Tilt-pair: the ID of the master image (the first entry).
Tilt (deg)	Out-of-plane tilt angle of the micrograph (in degrees).

In addition to the spreadsheet summary, an extended set of parameters of a selected micrograph (mouse LeftClick to highlight in the spreadsheet) can be accessed and edited in the Image Property group in the upper-right region of CP.

Above the spreadsheet, the project name and basic accounting statistics are displayed:

Project : the name of the project space.
Display : the image ID of the current display.
Total Images : the total image count in the project space.
Active Images : selected (active) image count in the project space.
Total Particles : the total particle count in the project space.
Active Particles : the particle count from active images in the project space.

Below the spreadsheet, a group of menu/button manages the data entry in the project space. From the left to the right, they are:

Imaging Setup : a pull-down menu that specifies the imaging geometry of the dataset in the project space. Single indicates that each micrograph is from independent single-exposure data acquisition, while TiltPair indicates that the data is from double-exposure tilted geometry (with the entries in the spreadsheet interleaved between the Master Image and the Pair Image).
+ : a button that imports ONE micrograph to the project space.
– : a button that deletes ONE micrograph from the project space (and the spreadsheet).
Monitor Mode : a pull-down menu that specifies the information display for the selected entry in the spreadsheet, in which Setup shows the detailed imaging parameters in the Image Property group; Micon displays a miniature of the micrograph for quick browsing; PSpec is the power spectrum of the micrograph (the power spectrum should be calculated beforehand during the CTF estimation).
Display : a button that loads and displays a selected (click on one spreadsheet entry) micrograph or image pair.
Stack : group all active particles in the project space into one stack (in the Single geometry) or a pair of stacks (in the TiltPair geometry).

It is highly recommended to save your project space from time to time (via the menu function MenuBar::Project::save), especially after a major modification to the data or before exiting PARTICLE. The project-space infrastructure is systematically named and managed by the program.

Demonstration

In PARTICLE, to set up a new project space:

Start the program, go to CP::MenuBar::Project::New, a browser window will pop up;
Choose a location (in your computer file system) for the new project space, e.g., in the folder "myProject";
Type "test" in the browser and press OK, then a project space named "test.em" (the extension "em" will be attached automatically if not specified) will be created in the "myProject" folder;
Move the demo dataset to the folder "test.em/micrograph";
Activate CP::MenuBar::Project::Data::Import, a list of recognized data images (T100[1-4].mrc) will be displayed in the editor at the upper-right region of CP;
Press the Import Data to Project Space button (on top of the editor) to enter all the images to the DataView spreadsheet;
Select the entry "T1001" via mouse LeftClick in the spreadsheet, then modify its imaging parameters (set Pixel-Size=2.00, Voltage=300, Magnification=60000) in the Image Property group (on the right of the spreadsheet);
Copy (via Image Property::Cp button) the imaging parameters of T1001 to all active micrograph entries in the project space, which will be updated instantly in the spreadsheet;
Optionally, take some quick Notes (e.g., for T1001, type in "tilt=0.0, paired with T1002"), and press the Save button (on top of the Notes box);
Save the current project space via CP::MenuBar::Project::Save.

Congratulations! A new project space has been created for the demo dataset, which is now accessible and managed by PARTICLE.