User Guide

Preprocessing of Race Tube Images

1. Crop your scanned race tube image as desired, in the image viewer program of choice, leaving a small amount of background on either long edge

2. No need to make your image greyscale, fix its rotation, or increase contrast- Rhythmidia will take care of all of this internally!

3. Race tube images can be .png, .tif, .tiff, .jpg, .jpeg, or .svg

Uploading and Analyzing an Image

1. Upon opening the software, you will be greeted with the “Home” tab, which will look like this:

2. To upload a new race tube image, click the button labeled “Upload Race Tube Image”

3. Rotate your image so that the growth direction of the tubes is from left to right across your screen

   1. To rotate your image 90 degrees clockwise, click the button labeled “Rotate”

4. If necessary, update the Time Sheet table to correspond to the times at which you marked your race tubes, located to the left of the image box

   1. Time Sheet entries are in days:hours:minutes, starting at 0:00:00 at the first time mark

   2. Entries past the greatest number of identified time marks in a single tube will be ignored, so there is no need to address them

5. When you are satisfied with your image’s orientation, click the button labeled “Lock & Analyze Image”

6. Rhythmidia will try to identify horizontal lines corresponding to the horizontal boundaries of the tubes in your image, including the lower and upper bounds below and above the final and first tubes

   1. One line between each two tubes

7. You will be directed to verify these lines:

   1. To remove an incorrect line, simply click on the line

   2. To add a missing line, simply click in an unoccupied position on the image

8. When you are satisfied with the positions of all tube demarcation lines, click the button labeled “Proceed”

9. Repeat steps 6-8 for time marks (red) and for bands (orange)

10. After you are satisfied with the positions of the bands and click “Proceed”, you will be able to see a preliminary calculation of the period of each tube below NOTE: if there is an issue at this stage (i.e. a missed or duplicated identifier) cancel image analysis and reload the image

11. You will now have the option to click the button labeled “Save Tubes to File” a. This will bring up a popup asking for a name for the pack of tubes in the current image before it saves them to file

    

    2. If you are working within an existing experiment file, this will simply add this pack to the file and update it

    3. Otherwise, you will be prompted to Save As a new experiment file for these tubes

The Experiment Tab

1. Whether opening an existing experiment file or working from a new pack image, granular experiment data, plots, and statistical analysis data are located on the Experiment tab

2. Experiment data (Entry, Pack, Tube # in pack, Period calculated 3 ways, and Growth rate) is located in the table in the top left

3. In the top right is the frame for statistical analysis of any number of tubes:

4. In the bottom half is the plot frame for plotting densitometry and a periodogram of a single tube:

5. At the bottom left is a button labeled “Display Pack Image”

   1. This button will display a popup window containing the greyscale version of the image corresponding to whichever pack is selected in the bottom left list that was the exact image used for analysis

Functions Overview

Open Experiment File (⌘O)

Close Experiment File (⌘C)

Save File (⌘S)

Save as… (↑⌘S)

Set working directory (⌘D)

Open graphics preferences (⌘P)