## The micrograph parameter hierarchy

The unit data element originating from an electron microscope is a micrograph. Typically, a collection of micrographs are taken of the same specimen, intended to be all processed in the same way. In Bsoft, this is defined as a "project", and is tied to a specific specimen produced in a specific manner under a specific set of conditions. Changing one single parameter in the production of the specimen constitutes a new project.

There are several instances where multiple micrographs are taken of the same field. Common examples are focal series and tomographic tilt series. Within a project, there is a grouping level called a "field", which contains all micrographs from the same field (also called a "field-of-view").

In single particle analysis (SPA), small images of single particles in each micrograph are extracted for further processing. In tomography, a subfield may also be extracted and accessed at this level.

The micrograph parameter hierarchy is therefore:

- Project

  - Field (Field-of-view)

    - Micrograph

      - Particle

      - Filament

        - Filament node

      - Structure factor

      - Layer line

      - Marker

- Reconstruction

  - Particle

  - Filament

    - Filament node

  - Structure factor

  - Marker

## STAR files for micrograph parameters (extension .star)

The STAR format defines a limited hierarchy, so that expressing the micrograph parameter hierarchy requires some specialized conventions. Each data block corresponds to a micrograph, and particle parameters are encoded in looped variables tightly linked to the original micrograph. Micrographs are identified by an "id" tag, and the fields-of-view they belong are identified by a "field_id" tag. Each particle is identified by a unique number, starting from 1 for the first particle in the micrograph:

> data_

> _micrograph.id <a string>

> _micrograph.field_id <a string>

> loop_

> _particle.id

> <numbers from 1 to n>

Parameters for the micrograph proper are encoded as tags with single values, such as the micrograph file name, the acceleration voltage and CTF parameters. Parameters for the individual particle images picked from a micrograph are encoded in a table-like construct starting with the keyword "loop_" followed by the list of tags and columns of values. The first column should always be the particle number starting with the first particle as one and referencing all the particles in the picked particle file. Any selections of particles should be done using a selection column (not by deleting and rearranging the particle records). The loop must be followed by an empty line to indicate its end. The start of a STAR file (before any "data_" keywords) is used to record the history of the file. Every program writing a STAR file should add comments to the end of this section giving the date and time and the command line for execution. Additional comments can be inserted at any point.

## XML files for micrograph parameters (extension .xml)

The same tags used for the STAR files are used in XML files (without the initial underscore). The micrograph hierarchy is better represented due to the inherent structure of the XML syntax.

## EMX (electron microscopy exchange files, extension .emx)

Selected parameters from the micrograph hierarchy can be exported to and imported from EMX files for interchange with other software packages. Because this is an evolving standard, it is likely to experience significant changes