From 2ff47b55e289edd3e4edca8bdbdd83092d0b4d20 Mon Sep 17 00:00:00 2001 From: RoccoDAnt Date: Mon, 7 Aug 2023 11:47:27 +0100 Subject: [PATCH] updated readme.md --- README.html | 12 ++++++++---- README.md | 11 +++++++++-- 2 files changed, 17 insertions(+), 6 deletions(-) diff --git a/README.html b/README.html index 88cf6c5..2f6dd39 100644 --- a/README.html +++ b/README.html @@ -29,7 +29,7 @@ codecov

ZELDA: a 3D Image Segmentation and Parent-Child relation plugin for microscopy image analysis in napari

Authors: Rocco D'Antuono, Giuseppina Pisignano

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Preprint: https://www.biorxiv.org/content/10.1101/2021.10.24.465596v1
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Article: Front. Comput. Sci., 04 January 2022 | https://doi.org/10.3389/fcomp.2021.796117
Examples of 2D and 3D data sets: https://doi.org/10.5281/zenodo.5651284

What you can do with ZELDA plugin for napari

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Installation

Option B. You can install napari-zelda also via pip. For the best experience, create a conda environment and use napari!=0.4.11, using the following instructions:

conda create -y -n napari-env python==3.8  
-conda activate napari-env  
-pip install "napari[all]"  
+conda activate napari-env
+conda install napari pyqt  
 pip install napari-zelda

Option C. Alternatively, clone the repository and install locally via pip:

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pip install -e .

Specifications

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pip install -e .

Option D. Get the latest code with git and pip:

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conda create -y -n napari-env python=3.8 git
+conda activate napari-env
+conda install napari pyqt
+pip install git+https://github.com/RoccoDAnt/napari-zelda.git

Specifications

This napari plugin was generated with Cookiecutter using with @napari's cookiecutter-napari-plugin template.

The GUI has been developed using magicgui widgets, while the image analysis and processing include functions from scikit-image, SciPy, and NumPy. Results are handled with pandas and datatable. Plots are obtained with matplotlib.