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Python scripts

This repository is a collection of python scripts that can be used to visualize data (Data exploration), check the image quality (ImageQuality), and to find the contours in a binary image (findContoursBinaryImage). The subprojects ImageQuality and findContourBinaryImage are in an alpha version and might not work properly. The Data exploration functions are ready to be used for data visualization.

Data exploration

This project contains the a python class DataExploration that can be used to create a histogram, violin plot, lmplot, and data descriptives. The CreatePCA, CreateTSNE, and CalculateSVD classes can be used to get an understanding of the variance in your data, as well as to identify potential outliers or batch effects. For a more detailed instruction on how to use these classes, please check the readme file in the folder Data exploration.

python-scripts's People

Contributors

tjmkuijpers avatar

Stargazers

Roman avatar

Watchers

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python-scripts's Issues

findContoursBinaryImage

Implement the following two calculations to identify the right spacing between objects:

  • Spacing between primitives that build a feature
  • Spacing between multiple features within on Image

createPCA

Function should be added to get the loading matrix (so we can identify the most relevant loadings)

createTSNE

perplexity is hard coded, no option to select the solver

createPCA

Different markers should be added to the 3D PCA plot

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