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---
title: ".txt file image compensation"
author: 'Vito Zanotelli et al.'
output:
  html_document:
    df_print: paged
    keep_md: true
---
# Aim
This shows how to compensate a .txt file using CATALYST

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Automatically run latex whenever a file changes: https://tex.stackexchange.com/questions/15342/automatically-start-the-necessary-pdflatex-runs-if-tex-has-changed-macos-x

latexmk -pdf -pvc file.tex

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# run: conda env create -f cp318_environment.yml
# run: conda env update -f cp318_environment.yml
# activate: conda activate cellprofiler318
name: cellprofiler318
# in order of priority: highest (top) to lowest (bottom)
channels:
  - anaconda
  - goodman # mysql-python for mac
  - bioconda
  - cyclus # java-jdk for windows

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asdf

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from skimage import color
def cmap_to_bw(cmap, minlight = 60):
    """
    Converts a hex colormap to a colormap of contrasting black and white colors.
    
    Args:
      cmap: a colormap as iterable of hex values, eg bokeh.palettes.plasma(10)
      minlight: a threshold for the lightness
    """
    cols = [tuple(int(h[i+1:i+3], 16)/256 for i in (0, 2, 4)) for h in cmap]