## Analysis Projects for New Members

**[A0] Project #A0 - Download MATLAB**

- Due to limited central lab desktop availability, if you have a capable laptop, please download the trial version of MATLAB here: https://www.mathworks.com/campaigns/products/ppc/google/matlab-trial-request.html?s_eid=ppc_5852767522&q=matlab%20trial%20version

**[A1] Project #A1 - MATLAB and Coding Basics**

- Open MATLAB (orange and blue conical icon on bottom). Also, go to the EMC Google Drive page and "$ Student Reports Summer 2016". This will the be the folder containing all the materials for the remaining projects. Go to "Project #A1".
- If you are new to MATLAB or would like a refresher before you start, go to: http://www.mathworks.com/help/matlab/getting-started-with-matlab.html?s_cid=learn_doc and look through the tutorials to the desired level of detail.
- Open the Excel file called “Sample_NEMO_Output.” This is a typical output from our main analysis program, containing the (x,y) coordinates of 21 evenly spaced points along the worm (worm is split into 20 even segments and coordinates of nodes are stored).
- Find the distance between two arbitrary points (x1,y1) and (x2,y2). (For all the assignments in A1 you may choose to write a MATLAB function to perform the task, or do it through your Command Window).
- It may be helpful to look through these spreadsheet-specific tutorials/documentation before you proceed with the assignment: http://www.mathworks.com/help/matlab/spreadsheets.html
- Estimate the length of a worm for a single frame (any frame is fine).
- Relevant documentation for next portion: http://www.mathworks.com/help/matlab/2-and-3d-plots.html
- Now find the average length of a worm over a time period (multiple frames) and plot length as a function of time in that time period. Include error bars, and please label the plots and display the units of measurement.

**[A2] Project #A2 - Image Processing with Matrices**

- Read this helpful article on images in MATLAB: http://www.mathworks.com/help/matlab/creating_plots/working-with-images-in-matlab-graphics.html, and then look around in the more general image documation here: http://www.mathworks.com/help/matlab/images_btfntr_-1.html
- Make an 800X800 pixels 2D binary image of a white circular disk of radius 200 pixels on black background.
- Go to “A2”. It should contain a binary image and a binary video.
- Find the centroid of the binary worm image, then convert this to spatial coordinates in mm (1mm=320 pixels) with the lower left corner of image as origin (as opposed to top left for row column image coordinates).

- Using the 2D binary video of a worm, plot the positions (X vs Y) of the worm’s center of mass in mm, this display is referred to as the track of the worm for the video. Account for the moving stage with the given stage coordinates of the respective video. The NEMO function which incorporates the stage data (you may want to look to this for guidance, is called segment_data and the stage data is stored in the array poffset).As always, please label the plots and display the units of measurement.

**[A3] Project #A3 - Data Fitting**

- Helpful reading: http://www.mathworks.com/discovery/data-fitting.html
- Go to "A3". It should contain a single sample laser data file, and a folder.
- With the sample laser intensity data (outside the folder), show the data and the fitted Gaussian on the same plot. Remember to always put units of measurement!
- Extract all the possible parameters from your Gaussian fit and output then in an excel file.
- Using the multiple laser intensity data (varied over wavelength), produce a plot of each of the extracted parameters as a function of wavelength.

**[A4] Project #A4 - Choosing your Program**

- At this point, you have completed the general data analysis training and have developed skills that will come in handy in your scientific career.
- Speak with a senior analysis team member to learn about the specific software we use in our lab, and you may begin getting familiar with anything that interests you.

**Congratulations! You have survived after extensive training to become an official member of the analysis team of the Elegant Mind Club. Now you are fully prepared to start your own project. Please go to the next page, Your Own Experiment.**