The SPIDER Reconstruction Engine

Table of Contents

How to run Spire
Projects in Spire
Project-wide parameters
Configuration of procedure files and directories
Configuration editor
Running SPIDER procedure files
The Project Viewer
The procedure file form
How to write SPIDER procedure files
File numbering
Additional options
The menus
Using an external project database
Some usefull graphical tools
Spire Tutorial


Spire provides:

Spire is designed to simplify running projects that consist of numerous SPIDER procedure files. Users who are new to SPIDER can quickly start processing electron micrographs. Spire provides a convenient environment for testing and debugging procedure files. However, Spire does not deal with program correctness per se - it simply runs your SPIDER procedure files, and saves a list of output files to a project file.

Note: Spire requires SPIDER version 13 or later.



The graphical interface is organized around dialogs, windows with buttons linked to SPIDER procedure files. Dialogs list a set of conceptually related procedure files, e.g., they may be organized around project subdirectories.

  • procedure files can be executed in SPIDER by pressing the button with the procedure file's name.
  • A procedure file can be edited with its accompanying Edit button.
  • The Help button opens a URL manual page with documentation about the procedure files in this dialog.
  • The appearance of dialogs is specified by the configuration, and can be changed in the configuration editor.

    External database

    Although Spire maintains an internal "database" of executed procedure files and their outputs, it may be interfaced to an external project database if your laboratory has one. While the Python coding depends entirely on the details of your local database, an API (Application Program Interface) is provided, along with example code for a MySQL project database. See Using an external database with Spire for details.


    You should have a working knowledge of the SPIDER operations that constitute the procedure files you're running. There is plenty of documentation:
    Spider home page
    A Quick Start Guide to Spider
    Spider User's Guide
    Spider Manual pages
    Reconstruction of Single Particles using Reference Projections (many example procedure files here!)

    How to run Spire

    At the Unix prompt, type:

    or, if you already have a project file, give the project filename as the first argument to Spire (no extension):
    spire proj0127

    Run it in background mode and you can still use the terminal:
    spire proj0127 &

    Next: Projects

    Updated 22 October 2018