Overview¶
VAMPIRE (Visually Aided Morpho-Phenotyping Image Recognition) analysis quantifies and visualizes heterogeneity of cell and nucleus morphology 1. It is used widely in analyzing microglial shape change in response to oxygen-glucose deprivation 2 and morphological changes in cancer metastasis 3.
vampire-analysis provides a reproducible, fully-documented, and easy-to-use Python package that is based on the method and software used the in vampireanalysis GUI 1. Main advantages include:
operating-system-independent package API
full documentation with easy-to-read code
flexible input and filtering options
flexible plotting options
Installation¶
See documentation for detailed installation guide. If Python is installed on your machine, type the following line into your command prompt to install via PyPI:
pip install vampire-analysis
Getting started¶
See documentation for detailed guide for basics of building and
applying models. If you have build.xlsx under C:\vampire
containing the build image set information, you can build the model with
>>> import pandas as pd # used to read excel files
>>> import vampire as vp # recommended import signature
>>> build_df = pd.read_excel(r'C:\vampire\build.xlsx')
>>> vp.model.build_models(build_df, random_state=1)
If you have apply.xlsx under C:\vampire containing the apply
image set information, you can apply the model with
>>> apply_df = pd.read_excel(r'C:\vampire\apply.xlsx')
>>> vp.model.apply_models(apply_df)
Flexible options are provided for building and applying models in the advanced section in the documentation.
References¶
- 1(1,2)
Phillip, J.M., Han, KS., Chen, WC. et al. A robust unsupervised machine-learning method to quantify the morphological heterogeneity of cells and nuclei. Nat Protoc 16, 754–774 (2021). https://doi.org/10.1038/s41596-020-00432-x
- 2
Joseph, A, Liao, R, Zhang, M, et al. Nanoparticle-microglial interaction in the ischemic brain is modulated by injury duration and treatment. Bioeng Transl Med. 2020; 5:e10175. https://doi.org/10.1002/btm2.10175
- 3
Wu, PH., Phillip, J., Khatau, S. et al. Evolution of cellular morpho-phenotypes in cancer metastasis. Sci Rep 5, 18437 (2016). https://doi.org/10.1038/srep18437