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VAMPIRE Image Analysis Package

Project description

VAMPIRE (Visually Aided Morpho-Phenotyping Image Recognition)

A robust method to quantify cell morphological heterogeneity

1. System requirements
OS : Windows 10 (64 bit) Version 1909
Software is not compatible with older versions of Windows.
Mac OS is not officially supported, but it may work when installed using pip.
Non-standard hardware is not required.

2. Installation Guide
Executable file option:
No installation required. Download the executable file from https://github.com/kukionfr/VAMPIRE_open/releases/download/executable/vampire.exe
Open the executable file to launch the graphic user interface (GUI) of the software\

PIP installation option:
Type the following into command prompt window to install vampireanlysis on PYPI (the Python package index) using pip installer

pip install vampireanalysis

To launch the GUI, type "vampire" into command prompt window.

3. Demo
Instructions to run on data can be found in the Procedure section of the manuscript.
Sample images to run VAMPIRE can be found in Supplementary Data: https://github.com/kukionfr/VAMPIRE_open/tree/master/Supplementary%20Data
Bigger dataset is also available in these two repositories:
1. https://github.com/kukionfr/Aging_human_dermal_fibroblast_nucleus
2. https://github.com/kukionfr/Micropattern_MEF_LMNA_Image
Expected output of the procedure is provided in the Figure 5 of the manuscript and also in the supplementary files.
Expected run time for demo :
Step 1-2, Segment cells or nuclei, 5~10 mins
Step 3, Create a list of images to build the shape-analysis model, 1-3 mins
Steps 4-9, Build shape-analysis model in VAMPIRE, 1-5 mins
Steps 10-12, Application of the model to analyze shapes across conditions, 1-5 mins
Total, steps 1-12, complete VAMPIRE analysis, 8-23 mins

4. Instructions for use
Instructions to run on data can be found in the Procedure section of the manuscript.
By following the Procedure section, the users can reproduce the expected output data provided in the supplementary files.

5. Code functionality
The source code can be installed using pip: “pip install vampireanalysis” for Python 3.6 or later.
After installation using pip, type “vampire” in the command window prompt to launch the GUI.\

• vampire.py : launch Tk interface for VAMPIRE GUI.
• mainbody.py : read the boundaries of cells or nuclei and process them through three key functions of VAMPIRE analysis: 1. Registration 2. PCA 3. Cluster.
• collect_selected_bstack.py : read the boundaries of cells or nuclei based on the CSV files that contains list of image sets to build or apply the VAMPIRE model.
• bdreg.py: register boundaries of cells or nuclei to eliminate rotational variance.
• pca_bdreg.py : apply PCA to the registered boundaries.
• PCA_custom.py : principal component analysis code.
• clusterSM.py : apply K-means clustering to PCA processed boundaries of cells or nuclei and assign the cluster number label to each cell or nuclei.
• update_csv.py : generate VAMPIRE datasheet based on the assigned cluster label
Codes that are not mentions here belongs to the codes explained. The provided explanation applies to those as well.\

Python library dependencies
pandas==1.1.0
numpy==1.19.1
scikit-learn==0.23.2
matplotlib==3.3.0
pillow==7.2.0
opencv-python==4.3.0.36
dask==2.22.0
scipy==1.5.2
scikit-image==0.17.2

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