xmipp3.protocols.protocol_create_gallery module

class xmipp3.protocols.protocol_create_gallery.XmippProtCreateGallery(**kwargs)

Bases: ProtAnalysis3D

Create a gallery of projections from a volume. This gallery of projections may help to understand the images observed in the microscope.

AI Generated:

## Overview

The Create Gallery protocol generates a systematic set of 2D projections from a 3D volume. These projections simulate how the structure would appear from different viewing directions, providing a direct link between the reconstructed volume and the particle images observed in the microscope.

For biological users, this protocol is especially useful for interpreting 2D class averages, validating reconstructions, or gaining intuition about the structural features of a macromolecule. By comparing experimental images with the generated projections, one can assess whether the reconstructed volume is consistent with the data and whether certain views are over- or under-represented.

This type of gallery is also commonly used for visualization, teaching, and figure preparation.

## Inputs and General Workflow

The protocol requires a 3D volume as input. From this volume, it computes projections over a range of orientations defined by the user.

The angular sampling is controlled by specifying ranges for rotational (in-plane rotation) and tilt (out-of-plane angle). The protocol systematically samples these angles to generate a grid of projections covering the orientation space.

If symmetry is present in the structure, it can be specified so that redundant views are avoided and the gallery reflects the true symmetry of the particle.

The output is a set of 2D images representing projections of the volume from different directions, which can be directly compared with experimental particle images or class averages.

## Angular Sampling: Exploring the Orientation Space

The most important parameters for biological interpretation are the angular ranges and steps.

The rotational angle typically spans 0 to 360 degrees and controls rotation around the projection axis. The tilt angle determines the viewing direction, where 0 degrees corresponds to a top view and 90 degrees to a side view.

The step size defines how densely the orientation space is sampled. Smaller steps produce a more detailed and complete gallery but increase computational cost and the number of generated images.

From a practical point of view, coarse sampling is often sufficient for e xploratory analysis or quick comparisons, while finer sampling is useful when trying to match specific experimental views or when preparing publication-quality figures.

## Symmetry Considerations

The symmetry group defines how orientations are reduced according to the intrinsic symmetry of the structure.

For asymmetric particles, the default c1 symmetry should be used. For symmetric assemblies (for example cyclic or dihedral symmetries), specifying the correct symmetry ensures that equivalent orientations are not redundantly sampled.

Biologically, this is important because symmetry determines which views are unique. Using the wrong symmetry may lead to misleading interpretations when comparing projections to experimental data.

## Projection Methods

The protocol offers several methods to compute projections, which mainly differ in computational approach and numerical properties.

The Fourier method is the default and most commonly used option. It computes projections using the central slice theorem in Fourier space and provides a good balance between accuracy and efficiency. For most biological applications, this is the recommended choice.

The Real space method performs projections by integrating along rays through the volume. It is conceptually straightforward but generally slower.

The Shears method is an alternative real-space approach that can be efficient in certain situations but is less commonly used in routine

workflows.

In most cases, users do not need to change the default method unless there is a specific reason to explore numerical differences.

## Advanced Parameters

Several advanced parameters are available, mainly affecting the Fourier-based projection.

The padding factor controls how much the volume is expanded before projection. Increasing padding can improve interpolation accuracy but also increases computational cost.

The maximum frequency defines the highest spatial frequency considered in the projection. Limiting this value can reduce noise or numerical artifacts but may also remove high-resolution information.

The interpolation method determines how values are estimated between sampled points. Higher-order interpolation (such as cubic B-spline) typically produces smoother and more accurate projections.

Another parameter, shift sigma, introduces small random shifts in the projections. While not commonly used in standard workflows, it can be helpful when simulating more realistic image variability.

For most biological use cases, the default values of these parameters are appropriate.

## Outputs and Their Interpretation

The protocol produces a set of 2D images corresponding to projections of the input volume. Each image is associated with a specific orientation, and together they form a gallery covering the sampled angular space.

These projections can be directly compared with experimental particle images or 2D class averages. Good agreement between projections and experimental data supports the validity of the reconstructed volume.

From a biological perspective, the gallery helps to: * Identify characteristic views of the structure * Understand how structural features appear in projection * Detect missing or underrepresented orientations in the data

## Practical Recommendations

A typical use of this protocol is to generate projections after obtaining a 3D reconstruction and compare them visually with 2D class averages. This helps verify that the reconstruction explains the observed data.

For exploratory analysis, moderate angular steps (for example 5–10 degrees) are usually sufficient. For more detailed comparisons or figure preparation, smaller steps may be beneficial.

If the structure has known symmetry, it is important to specify it correctly to avoid redundant projections and to obtain a biologically meaningful gallery.

In most cases, the default Fourier projection method with standard parameters provides reliable results without further tuning.

## Final Perspective

The Create Gallery protocol is a simple but powerful tool for connecting 3D structures with their 2D experimental observations. By visualizing how a volume appears from different orientations, it provides valuable intuition and serves as a practical validation step in cryo-EM workflows.

For biological users, it is often one of the most direct ways to assess whether a reconstruction truly reflects the underlying data.

INTERP_METHOD_BSPLINE = 2

INTERP_METHOD_LINEAR = 1

INTERP_METHOD_NEAREST = 0

METHOD_FOURIER = 2

METHOD_REAL_SPACE = 0

METHOD_SHEARS = 1

PARAM_FILE_NAME = 'projectionParameters.xmd'

copyInput()

createGallery()

createOutput()

interpMethodsDict = {0: 'nearest', 1: 'linear', 2: 'bspline'}