Case Study: Outlining Biological Tissues with the Polygon Tool

This case study explains how to use the polygon tool to trace the outlines of shapes. (You can download the original images here and the Quantius output data here.)

A common task in tissue engineering is to quantify the gross morphology of tissues. Automatic analysis of such tissues can be difficult due to non-ideal imaging conditions caused by thick samples, large variation between samples, and other context-dependent factors such as the presence of single cells, ragged tissue borders, out of focus light etc. Humans are excellent at making on-the-fly decisions about how to deal with these sources of variation.

In this example, we want to quantify the area of a growing epithelial tissue in order to characterize the bifurcation of the tissue into primordial lung buds.

From a set of very simple instructions, most workers correctly outline the object, even in the presence of various spurious features in the image set, such as disorganized masses of single cells and large local changes in image contrast.

We save image frames from a movie of mouse lung epithelium development as a set of .png files. The images are then uploaded to Quantius with the following parameters:

  • Job name: Epitheliumframes.
  • Tool: Polygon.
  • Slider: OFF.
  • Instructions: "Trace the outline of the smooth tubular object, ignoring the small particles around it. See the images above for what to do." (See the figure below.)
  • Replicates: 20.

Quantius workers are adept at detecting and outlining objects in difficult phase contrast settings. a Individual frames from a movie of a lung epithelial tissue growing in vitro are saved into a folder as a set of .png images. b Job setup parameters in the Quantius interface. c Overlay of raw outlines from a crowd of Quantius workers and cutom post-processing to extract a mean outline with error information. The relative fidelity of the crowd outline reflects the strengths of human annotation in overcoming difficulties in retrieving such outlining data from raw phase contrast image sets using standard automatic segmentation algorithms. d Tissue area calculations in FIJI based upon annotations by an expert scientist and those of a crowd of Quantius workers are in strong agreement.