Create and Run a Standard microCT Analysis

This is a step-by-step guide to running a standard microCT analysis using microCTr. It assumes you already have your data exported from the scanner into text files.

Create an RStudio Project

The first step is to create a folder that will contain your data and analysis.

First, open RStudio. Then, create a new RStudio project: File > New Project...

Select New Directory:

Select New Project:

Type the name of the folder you would like to create, and select the location you would like to create the folder. Then click Create Project:

You should now have a new folder which contains a .Rproj file with the name of the project and a .Rproj.user folder.

These are safe to ignore, but don’t delete or move them.

Generate Templates for Your Analysis

Click the Addins button at the top of RStudio:

Select microCT Genotype Comparison Setup or microCT Treatment Comparison Setup, depending on which type of analysis you are going to run.

You should now have two new files in your working folder, a .Rmd file labeled with today’s date and a data.xlsx file.

Prepare Your Data

The data.xlsx file is a template Excel file into which you should paste your data. There are separate sheets for Trabecular, Twice1, Twice2, and MFE data. Additionally, there’s a Key sheet.

The data sheets have green highlighted columns which indicate the data of interest. Examine these carefully to make sure there are not characters besides numbers (such as ! or ~), since this will affect the analysis. If any of these other characters are present, delete them, leaving only the number.

The data.xlsx file can be renamed whatever you want, but you will have to update this name in the final report. Don’t worry, I’ll show you how to do that when we get there.

The Key sheet is where you should specify the animal’s AS number, sex, group (genotype or treatment), sample number, and the measure numbers for the spine, metaphysis, and diaphysis. For example:

Prepare the Report

Now that the data are prepared, we’ll turn to generating the final report. Open the .Rmd file in RStudio. You can do this by clicking on the file name in the Files pane:

The .Rmd file is just a text file, and it should now be open for editing within RStudio:

Replace Template Title with the title you’d like to give the report, Your Name with your name, and The Date with today’s date. For example:

If you have changed the name of the data.xlsx file, here’s the place to update that information. Be sure to include the .xlsx file name extension!

Don’t change any of the other information at the top of the .Rmd file.

Optionally, you can add background information about the project to be included in the final report. Type it in the first section, in the lines between START BACKGROUND INFO and END BACKGROUND INFO. Don’t change anything else lower down in the file.

Make sure your file is saved by pressing Ctrl + S or clicking the Save button:

Now, generate the report by clicking Knit (or by pressing Ctrl + Shift + K):

After a few seconds, the final report should appear in the Viewer pane:

The final report is now in a .html file in your working folder:

You can do anything you would do with a regular file with this .html file: save it anywhere you like, attach it to an email, etc. You can also double click it to open it in your default web browser for easier viewing.