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tengjuilin / vampire-analysis

VAMPIRE (Visually Aided Morpho-Phenotyping Image Recognition) analysis quantifies and visualizes heterogeneity of cell and nucleus morphology.
https://vampire.readthedocs.io/en/latest/
GNU General Public License v3.0
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Help to run basic jupyter commands #8

Open anoshqa opened 7 months ago

anoshqa commented 7 months ago

Hi.

I have been spending the day installing vampire. Somehow pip install vampire-analysis works (atleast that doesnt give any error which pip install vampireanalysis is giving), which I believes installs this. But I am unable to run any commands from Jupyter like vp.build_model, extract properties or even vampire(). How to import this in jupyter or even run GUI from this? Help would be greatly appreciated.

tengjuilin commented 7 months ago

Hi, thanks for using vampire-analysis!

The package is currently under development. The most stable version can be installed with pip install vampire-analysis==0.1.0.dev11. When using it in Jupyter Notebook or Python scripts, you'll need to reference the submodules. For example,

import vampire as vp

vp.quickstart.build_model(...)

This implementation does not have a GUI - it's meant for high-throughput analysis with Jupyter Notebook only. If you wish to use a GUI, you can refer to the original paper and download from their repo.

anoshqa commented 7 months ago

Thank you very much for your quick reply! Wow. Finally it works (atleast my extraction.extract_properties worked and I got data). Now I have to figure out how to make one model as when I ran build_model, it told my model name ('test') wasn't defined. I was facing errors with original repo (maybe because of Microsoft studio etc). I am comfortable with jupyter, and indeed would like to run it through jupyter. I am now excited to run some commands on my data. Thank you again!