CellShape

Analysis of cell shape from 2D outlines in IGOR Pro.

Analysis | Outputs | Input Data

Analysis

A number of cell shape descriptors are analyzed. Note that the intended use of CellShape for analysis of cell outlines from single images of different cells grouped by experimental condition, i.e. it is not (currently) intended for use with movie-type data.

Briefly, violin plots where dots represent individual cells and the marker indicates the mean, show:

• minor axis length
• major axis length
• cell perimeter
• cell area (mask area is an equivalent metric)
• aspect ratio, minor:major axes
• symmetry, ratio of the cell area to the area of a the cell footprint reflected on its major axis
• convex area, area of a convex hull enclosing the cell perimeter
• solidity, ratio of cell area to convex area
• extent, ratio of cell area to the area of a bounding box
• maximum distance to the perimeter from the cell center
• minimum distance to the perimeter from the cell center

A plot of minor axis length vs major axis length. Each cell in the dataset is represented by a bubble, the size of which corresponds to that cell's area.

An image quilt to show the dataset.

If your data is appropriate and named correctly, a superplot can be made for all of the above listed violin plots.

Outputs

Example data is available in this repo together with example outputs.

A series of plots that compare the experimental conditions are generated.

Additionally, an image quilt of cell outlines is generated, this is maximized to show the most data possible while making same-sized quilts.

If your data are appropriate then superplot can be selected as an option (at the Alias Check stage).

Input data

Cell outlines are hand drawn by a user blind to the conditions of the experiment. We construct IMOD models - 1 model per image, multiple contours (outlines) per model. For input into Igor we need to convert each model to a text file using model2point. For example:

bash model2point -fl -ob -z example.mod example.txt

In the shell, a directory of models can be converted using:

bash find . -type f -name "*.mod" | while IFS= read file_name; do model2point -fl -ob -zc -ze "$file_name" "${file_name/mod/txt}" done

If using another package to generate the outlines, the text files need to be space delimited, with no header. Showing model contour x y z. For example:

0 0 104.00 1229.00 0.00 0 0 100.00 1225.00 0.00 0 0 100.00 1219.00 0.00

Running the code

1. Save CellShape.ipf in Wavemetrics/Igor Pro 8 User Files/User Procedures.
2. Open in Igor and compile.
3. Run using Macros>Cell Shape...
4. Select the folder of point files to be analysed.

Igor will determine the conditions, as long as the files are logically named (see ipf for details). Igor will ask in which order you'd like the outputs organised.

Next, you have the opportunity to rename conditions for the plots to make sense.

Click Do It and Igor will do the rest!