Common Operations Involving Microscopy Data

This package makes easy to replicate figures and movies from microscopy data from configuration files. It unifies loading image files of the data, with the option of locally caching the image retrieval, and it exports the data into several file formats. It currently supports image loading using different frameworks (see formats currently supported). It can also export image stacks of data as volumetric scalars using the OpenVDB format or VTK format for use in data manipulation and visualization software such as Paraview or Blender. The package is currently under active writing.

Table of contents

• Documentation
• Setup
• Features
• Status
• Contact
• License

Documentation

See documentation here

Setup

The package has been tested with versions of Python 3.9 and greater. The installation script will complain if either Numpy of Wheels is not installed Thus, make sure you have those dependencies installed first, or alternatively run: pip install wheels numpy && pip install imgfileops

Main libraries used

• BioIO (we use it for OME files in general)
• Pycromanager (for images saved with Micro-Manager)
• Tifffile (for generic tiff files, for image series when they are stored as individual files in a folder)

The package also uses other libraries. For a complete list, check the dependencies variable of the pyproject.toml file.

Features

Ability to write configuration files for volume export and movie rendering

This feature helps to programmatically render different versions of the data. For example, it is possible to export the data in volumetric formats using either OpenVDB or the VTK library. Similarly, it can render the data in a movie format using each channel separately, or in a composite image. For more details, see the project that consumes these configuration files: https://github.com/fabio-echegaray/movie-render. I'm currently working on the declarative grammar of this feature to make it consistent.

Formats currently supported

• ImageJ BiggTiff files using Pycromanager.
• MicroManager files .
  • Single stacks smaller than 4GBi using the Tifffile library.
  • Single stacks bigger than 4GBi using Pycromanager.
• Micro-Magellan files using the Tifffile library.
• Tiff files conforming to the OME-XML files using the BioIO library.
• Volocity files using the BioIO library.

To-do list for development in the future:

• Keep writting test functions (maybe generate a repository of image files to test against?).
• Write examples of file export.
• Improve exporting volumetric files and the related syntax in the configuration files.

Status

Project is active writing and in progress.

Contact

Created by @fabioechegaray

• fabio.echegaray@gmail.com
• GitHub Feel free to contact me!

License

ImgFileOps
Copyright (C) 2021-2025  Fabio Echegaray

This program is free software: you can redistribute it and/or modify
it under the terms of the GNU Affero General Public License as
published by the Free Software Foundation, either version 3 of the
License, or (at your option) any later version.

This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
GNU Affero General Public License for more details.

You should have received a copy of the GNU Affero General Public License
along with this program.  If not, see <https://www.gnu.org/licenses/>.