adyprat/smorph

Automated morphological analysis for cells

SMorph

This library automates the morphological analysis of cells and classify different subgroups based on the extracted morphometric parameters.

• The notebook single_cell_analysis.ipynb includes the morpholgy analysis to explore various morphological parameters of a single cell.

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Published Version

Please note that this is an update to the initial published version. If you prefer to use the published version please redirect to following commit hyperlink.

Published Version

• Follow the instructions there to setup and run the published version.

Git Commit ID: bc8a1cc20d66eca755cb1f0621a4df72ca665bda

Please note that the published version is not packaged as a library.

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Latest version usage

Quickstart

The package can be easily used in local and Colaboratory environment.

Colaboratory

Just go to following for:

• Single cell analysis:

• Group Cells analysis:

You'll have to upload you data to Colaboratory environment either directly to session storage or to your Google Drive.

Instructions for linking your Google Drive dataset:

• Either select Mount Drive from sidebar Files browser or manually execute the following code in a cell.

from google.colab import drive
drive.mount('/content/drive')

• After completing the authorization, paste the authorization code in the input.

• After confirmation, refresh the Files sidebar. Your drive would now be visible in it.

• Follow the same instructions in the following Usage instructions for organization of your data.

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The same notebook can also run on your local environment.

Installation from source

The code has been tested for Python 3.7.11 and above, if you don't have it installed, please download the binaries from here and follow the installation guide.

SMorph uses Poetry package manager. Use the package manager pip to install Poetry. And install the dependencies by typing following in the command line:

pip install -r requirements.txt
poetry install

If the above commands throw errors on windows, please try:

python -m pip install -r requirements.txt
poetry install

Setup for analysis on local environment

To run the notebooks, execute following from command line and locate to the desired notebook using browser.

poetry shell
jupyter notebook

If the above command throw errors on windows, please try:

poetry shell
python -m notebook

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Usage

Group analysis

• Place your image data folders inside the Datasets folder, with each group's images organized in their respective folders.

• Run the analysis by replacing the value of groups_folders variable in group_analysis.ipynb with path to each of your cell groups.

Single cell analysis

• Run the analysis by replacing the value of cell_image variable in single_cell_analysis.ipynb with path to your cell image.

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Help & Support

• If you encounter a previously unreported bug/code issue, please post here (we encourage you to search issues first): https://github.com/swanandlab/SMorph/issues

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References

If you use this code and find it useful, we kindly ask that you please cite

Parul Sethi, Garima Virmani, Kushaan Gupta, Surya Chandra Rao Thumu, Narendrakumar Ramanan, Swananda Marathe. Automated morphometric analysis with SMorph software reveals plasticity induced by antidepressant therapy in hippocampal astrocytes. J Cell Sci 15 June 2021; 134 (12): jcs258430 https://doi.org/10.1242/jcs.258430