Track-A-Worm (version 2.0)
Version 2 has the following major new features:
1. Automatic spline fitting can now be done accurately for all kinds of worm shapes except for some challenging omega-shapes. Many omega-shapes can also be resolved.
2.You can now configure TTL signals using the Record module to control external devices (e.g., laser generators). Up to 3 different devices may be controlled independently in any on-and-off patterns. This feature may be conveniently used for optogenetic stimulation.
3. A new module allows the quantification of worm curvatures at various positions along the body axis.
4. The ventral and dorsal sides of a worm can now be marked at the beginning of each recording. This feature is especially useful for detecting curvature differences between ventral and dorsal sides.
5. The number of frames that can be included in each recording is now very large. You can recorded for essentially as many frames as you wish.
6. The Fit Spline window can now be resized to match any monitor size.
Note: 1. The hardware NI myDAQ (~$200, National Instruments) is required for generating the TTL signals. 2. The software has been tested with only Matlab2013a running in Windows 7 (64-bit). 3. Additional information about Track-A-Worm may be found at www.trackaworm.com.
Procedures for installing Track-A-Worm v2:
1. Download the free Matlab Compiler (R2021b, 64 bit for Windows). This step may be omitted if you already have Matlab installed on your computer.
2. Download the Track-A-Worm v2 (a compressed file).
3. Decompress the installer and install it.
Baseline
This MATLAB-based app allows you to correct the drop in fluorescence signal over time due to photobleaching of a genetically encoded calcium sensor such as GCaMP6. The software uses the cubic interpolation algorithm to create a curve along the baseline chosen by the user. Subsequently, the raw data are divided by the interpolated points of the baseline to generate the normalized data. The software may be used by following these steps: 1) Assign regions of interest (ROIs) in your calcium imaging data using ImageJ (National Institute of Health); 2) plot fluorescence intensities (F) in each ROI as absolute intensities over time; 3) save only the fluorescence intensities as a text file; 4) run the app by clicking the "baseline.m" file; 5) load the text file into the app to produce a trace of the raw data; 6) click baseline points along the plot while holding down the "Alt" key, followed by clicking "Done"; 7) Click "Yes" if the spline (red color) generated by the app represents the baseline well; 8) save the data (F/F0). Click baseline to download the app.
