Rem2 mouse imaging

Data storage

Data location

Data will be stored on On the Mac, connect to, log in with your KFC username and password, and mount Data3. Our folder is Paradis_VanHooser.

Transferring data to our data folder from the experiment rig at the end of the day

It is imperative that we transfer our experimental data off of the acquisition machines so 1) the acquisition machines will have sufficient disk space during experiments, and 2) so it can be housed more safely and won't be accidentally deleted in the heat of an experiment.

Follow the following steps to transfer data from the master computer Leghorn:

The easiest way to accomplish this from a Windows machine (both of our master computers Foghorn and Leghorn are Windows machines) is the following:

    1. Run cygwin (application is on the desktop)

    2. Change directories to the remote directory where experimental data comes in by entering the command cd C:\remote

  1. From cygwin on the windows machine, copy the directory using scp, using your own day's directory name in place of 2011-05-35: scp -r 2011-05-35

  2. Update the permissions using the command ssh chmod -R 775 /Volumes/DataDrive3/Data3/Paradis_VanHooser/2011-05-35

  3. Verify that your data has transferred by checking kfc, and then remove the data from the master computer (Foghorn or Leghorn)


To make a new log, 1) open the template and 2) save a new copy (BE SURE TO ACTUALLY SAVE A NEW COPY!). Save a new copy in the shared Google doc directory. (Need access? Email Steve) When you make your log, you can put a link to it below so we can all read it.

Link to Google Drive folder of surgery and imaging logs:

Notes on quality of experiments:

Experiment parameters:

Updated Mouse Surgery Log: page 2 and page 1

Updated Mouse Surgery Log V2: pages 1 and 2

*For best results, download logs, then print*

Mouse Virus Surgery Log for two mice


How to run things

Retinotopy stimulus

  1. The monitor should be centered in the animal's gaze. Imagine a straight line coming off the animal's nose. If this is not possible, then measure where a straight line coming off the animal's nose hits the stimulus monitor (how far is this from the left in cm?) Measure it and write it in the log.

  2. The retinotopy stimulus is on the "Chr2" Sheet. You can open this sheet by selecting it from the "Active Sheets" on the RunExperiment window.

  3. Click "edit base" to edit the base grating stimulus.

    1. Set contrast to 1

    2. Set temporal frequency to what you are using (2 Hz?)

    3. Set spatial frequency to what you are using (0.04 cycles per degree?)

    4. Set number of cycles to 10

    5. Set number of loops to 1 (should already be set this way). This will loop the stimulus back and forth once (moving the gratings back and forth)

    6. Set angle to 90

    7. Click "OK"

    8. Set the number of repetitions to 12 (10 might be okay). Set the interstimulus interval to 5.

    9. Under "Retinotopy" set the parameters to the following: [0 100 800 100 1]

    10. Click Run


    1. Start with a directory that has been completely curated (that is, all cells have been drawn, all "analyze by param" or "stim" have been run), and cells have been added to the database.

    2. Use the function mouse_tp_addvariables to add the animal parameters to your directory. See help mouse_tp_addvariables for documentation, an example is here:

    3. mouse_tp_addvariables('/Volumes/Data3/Paradis_VanHooser/2014-09-07',32,'','RI192',[],[],'none',[],[],'Rem2 Insert',7,'left');

    4. Actually perform the fitting and analysis using the function analyze_mouse_tp. Example:

    5. analyze_mouse_tp('/Volumes/Data3/Paradis_VanHooser/2014-09-14',1,1,0);

  1. When you are all done, you can add those directories to the analysis program in mousevision_plots.m, and you can run it with:

    1. mousevision_plots(0)