Coloring by properties (float)

vzinche · March 4, 2021, 8:14am

Hi napari ppl,

Is it currently possible to color a label layer by a property that is continuous?
Let’s say I have a cell segmentation, and I want to color it by cell size.

Is there any easier way to do it that manually mapping sizes to colors in a color dict?

Many thanks

VolkerH · March 4, 2021, 9:47am

Hi Valentyna,

yes, there is an easy way using scikit image’s map_array. Give me a few minutes and I will provide an example.

VolkerH · March 4, 2021, 3:09pm

Here is an example notebook

gist.github.com

https://gist.github.com/VolkerH/465925d24accc940f7a0a0b1f5f40f7a#file-map_array_example-ipynb

map_array_example.ipynb

{
 "cells": [
  {
   "cell_type": "code",
   "execution_count": 1,
   "id": "satellite-momentum",
   "metadata": {},
   "outputs": [],
   "source": [
    "import napari\n",

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Note that this is also useful if you want to filter out labels based on several measurements.
You can turn the regionprops into a pandas DataFrame, do your filtering (i.e. a new column that only retains the labels you want to keep) and map this to a new label image.

vzinche · March 4, 2021, 12:02pm

Hi Volker,

That’s really neat, thanks a lot!