https://github.com/alexiatiberi/ymaze
Short python code to analyze YMaze sequences of arm entries -- an easy way to get the alternation index for a Y maze behavioral assay.
Science Score: 13.0%
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Low similarity (7.9%) to scientific vocabulary
Repository
Short python code to analyze YMaze sequences of arm entries -- an easy way to get the alternation index for a Y maze behavioral assay.
Basic Info
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- Stars: 0
- Watchers: 1
- Forks: 0
- Open Issues: 0
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Metadata Files
README.md
As neuroscientists, we are probably all familiar with the Y maze test, a test to evaluate spatial working memory in mice.
To put it simply, the mouse is put in a maze, which unsurprisingly has a Y shape, and the researcher must record the sequence of arm entries during a mouse exploration of the maze. Here's the maze:
In this test, a mouse has performed well if it has alternated between arms - for example if it enters a then b then c, while it is considered to have performed poorly if it does something like "ccbcbc" as a sequence of arm entries. To quantify the performance, we usually report both the total number of entries (to account for general motility) and Spontaneous Alternation% defined as 100 x number of correct alternations/total number of entries. Since I got bored with getting the data by hand (it was enough that I had to watch a mouse for five minutes and record on a piece of paper where the little thing went), I wrote this very easy code to get data from a string of "abc" corresponding to the arm entries in a Ymaze:
In the 2.0 version, you get asked where you want to save your analysis first: just paste in the path from the address bar. Type n to enter a new pair of animal code/string. The program asks to enter the code that identifies the animal
Ex: Animal code: Cage1m1DOB19/02/2020
And the string corresponding to the arm entries
Ex: String: abcbacbabcbacbbacbbabacbacbac
After entering all your data type quit to exit the program. The program outputs a csv file (named "ymazeanalysis") containing the number of entries, the number of correct alternations and finally the alternation index, together with the given animal code and string.
Python version: 3.7.6
Owner
- Name: Alexia Tiberi
- Login: AlexiaTiberi
- Kind: user
- Twitter: Alexia_Keira
- Repositories: 1
- Profile: https://github.com/AlexiaTiberi
Neuroscience. Postdoc naively approaching coding. #notacoder Mostly bored with doing everything by hand. CNR, Institute of Neuroscience, Pisa, Italy