This guide is for people who need to manually score rearing behavior in videos of rats.Â
    To analyze rearing behavior in a video, you will need to use MATLAB and the video files - after running the video through MATLAB.
This instruction is still under construction. If anything is unclear to you, slack Dylan, Billy, Gavin, Hira, or Luca on NewmanLab slack channel.Â
Open the necessary items:
(1) computer's File Explorer
(2) the tracking sheet (listed as MS 40-49trackingsheet as a .XLSX file on Newman Lab's Google Drive - make sure you are logged into the lab gmail account (newmanmemorylab@gmail.com).)
(3) MATLAB (*Use R2021a program, which should be pinned onto the computer's lower desktop gray bar)
(4) an empty paper sheet or Google Doc.
Check the MS 40-49trackingsheet in the Google Drive and select a box - which correlates to a specific video within the file - that has not been done yet (not highlighted in green).
*Use the gray bar on the bottom of the page to go through MS 40 through MS 49.
Find the appropriate date of the video selected (located in the third column of the MS 40-49trackingsheet under Date of Video/Collected).
For example, 4/13/2023 in MS 40
Go to the computer's File Explorer, and find the appropriate location of the selected video.
file location: ~\Dropbox (NewmanLab)\ratsEphys\ChATChR2onHPC_MS##_halo\{date of your selected video}
For example: ~\Dropbox (NewmanLab)\ratsEphys\ChATChR2onHPC_MS40_halo\230413
Underlined: this is based on which MS ## you choose, and the date you choose
Under file location: ~\Dropbox (NewmanLab)\ratsEphys : there will be MS 40 through MS 49 listed as ChATChR2onHPC_MS40_halo, ... , ChATChR2onHPC_MS49_halo.
After finding the appropriate MS ## file location, the date of your selected video will be under the file folder listed as the last 2 digits the year selected, the month in 2 digits, and the date in 2 digits without any slashes and/or dashes
For example, 4/13/2023 will be in file '230413'
After finding the appropriate file location, find your selected video
The video should be listed as the date in the formatted as 'Full Year-Month-Date ...'
For example, 4/13/2023 will be in file '2023-04-13 ... '
*Do not use the videos that has word 'converted'
*If there is the same video file with the difference of the word 'top' or 'side', use the video that uses the word 'top' for the top view of the video
After finding your selected video, first left-click to select your selected video, then right-click the selected video file, then go to 'Open with', then 'Choose another app', and choose 'djv' to open this selected video file.
*If you do not see 'Open with' after right-clicking, then double left-click the selected video to play the original downloaded selected video file, then close out of the tab, then try the left-click process again
After opening the djv file of your selected video, find the total frames in the video, and record the number in your empty paper/Google Doc.Â
*If you cannot open the djv file at first, then open the actual video (typically mp4 file) first, wait for the actual video to load and start playing, then try opening the djv file again!
Number for total frames in the video is located on bottom right-hand corner of the djv file.
Start playing the djv file of the selected video and record all the start and end frames every time the rat displays rearing behavior - during each trial/testing time (2 total trials/testing times in each video) - pause and/or rewind the video as needed!
*If person is in frame while rat is rearing, that rearing does not count!
*Keep track of the total number of times the rat displays rearing behavior in the entire video during the 2 total trials/testing times (finding what each trial looks like, refer the instructions 'To manually score for start and end times of each test/trials (using MATLAB and video files)' below)
*Each rearing behavior time should be a pair of numbers, in the format of 'frame number when starting rearing behavior : frame number when ending that rearing behavior'
Frame number of the video when playing should be displayed on the right-side of the cursor of the djv video
*Subtract 5-10 frames depending on personal reaction time
Start of rearing behavior: when the rat is halfway up from fully standing on its hind legs.
End of rearing behavior: when the rat puts its front paws fully down onto the ground of the maze
After the djv video ends playing and after finding all the rearing behavior times as needed, open MATLAB, and press 'Run', then fill out the listed questions
*Make sure the file is saved to the appropriate file space
file location: ~\D:\Dropbox (NewmanLab)\ratsEphys\ChATChR2onHPC_MS##_halo\{date of your selected video}
For example, file location: ~\D:\Dropbox (NewmanLab)\ratsEphys\ChATChR2onHPC_MS40_halo\230413
Listed questions
>> inputrearframes
How many total frames are in the video: (recorded number from Step 7)
How many rears are there in the video: (first bullet point under Step 8)
Enter index pair values (#/ number from above questions): (pair of numbers from Step 8)
Put a colon ':' without spaces in between the pair of numbers to separate it, then press 'Enter' to go enter the next pair of numbers)
What do you want to name the file? "(name of selected folder_(Trial Type)_rearframes.csv"
Click 'Enter' to finish
After finishing, check the original selected video file location in File Explorer to see if the .csv file is correctly named and saved
Go back to the MS 40-49trackingsheet in the Google Drive and highlight the appropriate date box in the 'Video scored for rearing' column in green.
Open the necessary items:
(1) computer's File Explorer
(2) the tracking sheet (listed as MS 40-49trackingsheet as a .XLSX file on Newman Lab's Google Drive - make sure you are logged into the lab gmail account (newmanmemorylab@gmail.com).)
(3) MATLAB (*Use R2021a program, which should be pinned onto the computer's lower desktop gray bar)
(4) an empty paper sheet or Google Doc.
Check the MS 40-49trackingsheet in the Google Drive and select a box - which correlates to a specific video within the file - that has not been done yet (not highlighted in green).
*Use the gray bar on the bottom of the page to go through MS 40 through MS 49.
Find the appropriate date of the video selected (located in the third column of the MS 40-49trackingsheet under Date of Video/Collected).
For example, 4/13/2023 in MS 40
Go to the computer's File Explorer, and find the appropriate location of the selected video.
file location: ~\Dropbox (NewmanLab)\ratsEphys\ChATChR2onHPC_MS##_halo\{date of your selected video}
For example: ~\Dropbox (NewmanLab)\ratsEphys\ChATChR2onHPC_MS40_halo\230413
Underlined: this is based on which MS ## you choose, and the date you choose
Under file location: ~\Dropbox (NewmanLab)\ratsEphys : there will be MS 40 through MS 49 listed as ChATChR2onHPC_MS40_halo, ... , ChATChR2onHPC_MS49_halo.
After finding the appropriate MS ## file location, the date of your selected video will be under the file folder listed as the last 2 digits the year selected, the month in 2 digits, and the date in 2 digits without any slashes and/or dashes
For example, 4/13/2023 will be in file '230413'
After finding the appropriate file location, find your selected video
The video should be listed as the date in the formatted as 'Full Year-Month-Date ...'
For example, 4/13/2023 will be in file '2023-04-13 ... '
*Do not use the videos that has word 'converted'
*If there is the same video file with the difference of the word 'top' or 'side', use the video that uses the word 'top' for the top view of the video
After finding your selected video, first left-click to select your selected video, then right-click the selected video file, then go to 'Open with', then 'Choose another app', and choose 'djv' to open this selected video file.
*If you do not see 'Open with' after right-clicking, then double left-click the selected video to play the original downloaded selected video file, then close out of the tab, then try the left-click process again
After opening the djv file of your selected video, find the total frames in the video, and record the number in your empty paper/Google Doc.Â
*If you cannot open the djv file at first, then open the actual video (typically mp4 file) first, wait for the actual video to load and start playing, then try opening the djv file again!
Number for total frames in the video is located on bottom right-hand corner of the djv file.
Start playing the djv file of the selected video and record all the start and end frames every time the trial/testing times starts and ends (2 total trials/testing times in each video) - pause and/or rewind the video as needed!
Start of trials/testing times: when the lab technician fully leaves the frame of the video - after putting the rat down onto the maze
End of trials/testing times: when any part of the lab technician enters into the frame of the video
Frame number of the video when playing should be displayed on the right-side of the cursor of the djv video
Start and end of trials/testing times will be one pair of values, there should be 2 pairs of values in total
*Subtract 5-10 frames depending on personal reaction time
After the djv video ends playing and after finding all the trials/testing times as needed, open MATLAB, and press 'Run', then fill out the listed questions
*Make sure the file is saved to the appropriate file space
file location: ~\D:\Dropbox (NewmanLab)\ratsEphys\ChATChR2onHPC_MS##_halo\{date of your selected video}
For example, file location: ~\D:\Dropbox (NewmanLab)\ratsEphys\ChATChR2onHPC_MS40_halo\230413
Listed questions
>> inputrearframes
How many total frames are in the video: (recorded number from Step 7)
How many rears are there in the video: 2
This number will always be 2
Enter index pair values (#/ number from above questions): (pair of numbers from Step 8)
Put a colon ':' without spaces in between the pair of numbers to separate it, then press 'Enter' to go enter the next pair of numbers)
This number will always be 2 sets of pairs, so 4 numbers total!
What do you want to name the file? "(name of selected folder_(Trial Type)_startend.csv"
Click 'Enter' to finish
After finishing, check the original selected video file location in File Explorer to see if the .csv file is correctly named and saved
Go back to the MS 40-49trackingsheet in the Google Drive and highlight the appropriate date box in the 'Study/test start and end' column in green.