etomofiles

A Python package for reading IMOD etomo alignment files into pandas DataFrames.

Overview

etomofiles provides a way to extract metadata from etomo alignment directories and convert them into structured pandas DataFrames.

Installation

pip install etomofiles

Quick Start

import etomofiles

# Read etomo alignment data
df = etomofiles.read("/path/to/etomo/directory")

print(df.head())

DataFrame Columns

The resulting DataFrame contains the following columns:

Column	Description
`image_path`	Path to specific image in tilt series (e.g., `TS_001.st[0]`)
`idx_tilt`	Index of the tilt image (0-based)
`tilt_axis_angle`	Tilt axis rotation angle (degrees)
`rawtlt`	Raw tilt angle (degrees)
`tlt`	Corrected tilt angle (degrees)
`xtilt`	Tilt around x-axis
`xf_a11`, `xf_a12`, `xf_a21`, `xf_a22`, `xf_dx`, `xf_dy`	xf transformation matrix elements
`excluded`	Boolean indicating if view was excluded

xf Utilities

Get xf as numpy array:

import etomofiles

# Read alignment data
df = etomofiles.read("TS_001/")

# Get xf as numpy array:
xf_matrices = etomofiles.df_to_xf(df)

# Each matrix represents an affine transformation:
# [[A11, A12, DX],
#  [A21, A22, DY]]
# where X' = A11*X + A12*Y + DX
#       Y' = A21*X + A22*Y + DY

# Also works directly with files
xf_matrices = etomofiles.df_to_xf("TS_001/TS_001.xf")

# Choose row ordering convention
xf_xy = etomofiles.df_to_xf(df)  # default xy
# Each matrix is [[A11, A12, DX], [A21, A22, DY]]

xf_yx = etomofiles.df_to_xf(df, yx=True)  # yx
# Each matrix is [[A22, A21, DY], [A12, A11, DX]]

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Attestations: Values shown here reflect the state when the release was signed and may no longer be current.

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Source repository:
- Permalink: teamtomo/etomofiles@ef39d9e9749292fa246f5827876f6f69818256bd
- Branch / Tag: refs/tags/v0.1.2
- Owner: https://github.com/teamtomo
- Access: public
Publication detail:
- Token Issuer: https://token.actions.githubusercontent.com
- Runner Environment: github-hosted
- Publication workflow: ci.yml@ef39d9e9749292fa246f5827876f6f69818256bd
- Trigger Event: push

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0.1.2 This release

Jun 30, 2026 2 files

0.1.1

Oct 22, 2025 2 files

0.1.0

Aug 28, 2025 2 files

etomofiles 0.1.2

etomofiles

Overview

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DataFrame Columns

xf Utilities

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