ActinMeshure: Quantify cytoskeletal actin remodelling#

AchinMeshure is a small library of functions which aim to quantify actin remodelling from super-resolution microscopy images of cytoskeletal actin.

The library includes classes and helpers to:

  • read in images and extract metadata into ActImg instances

  • manipulate, visualise, and save images in either ActImg or ActImgBinary instances; also great for interactive analysis

  • run batch analyses on entire directories with data using the ActImgCollection class

  • summarise and visualise batch processing results, written into HTML files (requires Pandoc)

Installation from source#

To install ActinMeshure, download the source code from the repository, navigate to the destination directory, and run:

$ pip install .

If you wish to edit/develop the package, run it directly from source using:

$ pip install -e .  # Run once to add package to Python path

License#

Copyright 2023, Simoncelli Lab.

Licensed under the Apache License, Version 2.0 (the “License”); you may not use this file except in compliance with the License. You may obtain a copy of the License at http://www.apache.org/licenses/LICENSE-2.0.

Unless required by applicable law or agreed to in writing, software distributed under the License is distributed on an “AS IS” BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the License for the specific language governing permissions and limitations under the License.

Citation#

If you find this project useful to your work, please, cite it as:

Radoykova, S., 2023. ActinMeshure: Quantify cytoskeletal actin remodelling. https://github.com/sedaradoykova/actin_mesh_measures

For installation and getting started, see Installation. Read more detailed installation instructions in Getting started. For tutorials, refer to the tutorials included in this documentation.

Warning

This library is under development.

Getting started:

Tutorials:

Meshure classes: