Getting started with Xmipp

Suggested reading

You are invited to read the Xmipp3.0 presentation to clarify the general concepts about the package.

Download and Install

Xmipp is now integrated into Scipion . We recommend that you install Scipion and run Xmipp inside it.

If you need to run old Xmipp, read [[HowToInstall]how to install Xmipp 3.1]].

Creating the Project

Be sure you have Xmipp properly installed. Go to the desired folder where you want to create your new project and type xmipp_protocols. After that, you will be requested to confirm the project creation. Just press Enter and an empty project will be created. The project GUI will appear.

Importing data

Following is an overview of importing and preprocessing data before continue with 2D and 3D steps.

Project GUI

After some working, you will find your project populated with several runs of different protocols. You can find more information about project and protocols gui in the topic Working with Protocols. Your project GUI will looks like this:

Launching a Protocol

When you select to create some protocol run from the left panel, a protocol GUI will show up. From this GUI you will be able to select the input values to launch the protocol.

Using Wizards

The wizards are simple but useful GUI that will guide you to select some parameters. Following is the wizard that helps on selecting downsampling factor and frequencies cutoff on CTF estimation.

The project Browser

Another useful tool is the browser, which is a normal file browser but it recognizes several images formats, stacks, Xmipp's metadatas and other. It also displays a preview of the selected object and can open files with our visualization tools.

Xmipp Programs inside the Project

Although protocols are predefined workflows involving several programs and steps, you can use all Xmipp programs inside your Project. When you click on the Xmipp Programs button on the left panel you will search between all programs and launch the desired one. You will get a lauch GUI just like any other protocol and the same trace.

Short guide of Programs

You can also use the programs GUI outside the Protocols, using the options --gui, other useful option is --more for displaying more information. The examples section shows you most common uses. In the following page you can find the complete List of Programs. Just to mention some of the them:

Visualizing data

Most of the programs information is now stored in metadatas, which are text files base on the STAR format. These metadatas can bee seen as tables, with colums (or labels) and rows of data. The xmipp_showj program can visualize this data in a nice way.

Some of the column (paths to images, volumes, stacks) can be rendered. Checking the option Display -> Render labels you will see a preview of them in the table view.

Or even display like a gallery of images. This is the same way that volumes are viewed (gallery of slices) or stacks.

You can find more information about the use of showj in the topic Using showj