“A time memory engram embedded in a light-entrainable circadian clock” David E. Ehichioya1, S. K. Tahajjul Taufique1, Sofia Farah, Shin Yamazaki - Current Biology

[March 1, 2024: Bug-fixed version of FED3.cpp uploaded]

Raw ClockLab and FED3 Data Description:
FED3 data was converted to text file format which can be directly open by the ClockLab.
Experimental conditions are indicated in the excel file in each data holder.

FED3 Run Code Description:

“FED3_1.16.1_RF.ino”: a code written specifically for controlling FED3 hardware such as a stepper motor which rotates a disk attached and then dispenses a pellet. It is written using Arduino Integrative Development Environment (Arduino IDE), an open-source platform that uses a programming language based on C++. The “FED3_1.16.1_RF.ino” is a modified version of the original code (“Timed_FR1.ino” with FED3 1.16.1) to enable the feeding schedule cross the midnight (the time date change occurs). For instance, a FED3 feeding schedule from 22:00 to 2:00 cannot be programmed by the original code). With this modified code, the feeding schedule can be programmed as 22:00 to 26:00 and the FED3 provides a continuous feeding window from 22:00 to 2:00.

"FED3.cpp": a code written by C++ containing user-defined functions which are declared within a class (FED3) in the "FED3.h" header file. The "FED3_1.16.1_RF.ino" file calls the class FED3. The “FED3.cpp” and “FED3.h” files are written separately from “FED3_1.16.1_RF.ino” otherwise complicated in a single ino file. Arduino IDE compiles all three files and uploads them onto the FED3 Arduino board (Adafruit Feather M0) which is connected to a PC via a USB cable. We deactivate buzzer and LED lights in the modified FED3.cpp. We also modified FED3.h to display a FED3 version with “RF” extension.

FED3 Data Converter Description:

“FED3_analysis_v1.4.3.py”: a code written for the analysis of data downloaded from the FED3 SD card. It is written using python 3.11.4. This code converts the FED3 data to the text file format which can be opened by the ClockLab.

[2024年3月1日：修复版FED3.cpp已上传]

原始ClockLab与FED3数据集说明：
FED3数据已转换为可直接由ClockLab打开的文本文件格式。各数据集文件夹中的Excel文件标注了实验条件。

FED3运行代码说明：

"FED3_1.16.1_RF.ino"：专为控制FED3硬件而编写的代码，可驱动带动圆盘旋转的步进电机以分发实验用颗粒食丸。该代码基于开源平台Arduino集成开发环境（Arduino IDE）编写，其编程语言依托C++实现。此版本是对原始代码（适配FED3 1.16.1的"Timed_FR1.ino"）的修改版，新增了跨午夜的实验喂食计划设置功能（原始代码无法实现如22:00至次日2:00的喂食计划编程）。通过该修改版代码，可将喂食计划设置为22:00至26:00，从而实现22:00至次日2:00的连续喂食窗口。

"FED3.cpp"：基于C++编写的代码，包含在"FED3.h"头文件中以类（FED3）形式声明的用户自定义函数。"FED3_1.16.1_RF.ino"会调用该FED3类。将"FED3.cpp"与"FED3_1.16.1_RF.ino"分离编写，可避免单个ino文件内代码过于复杂。Arduino IDE会编译这三个文件并上传至通过USB线缆连接至PC的FED3 Arduino开发板（Adafruit Feather M0）。本次修改中，我们禁用了FED3.cpp中的蜂鸣器与LED指示灯，并修改了FED3.h以显示带有"RF"后缀的FED3版本标识。

FED3数据转换工具说明：

"FED3_analysis_v1.4.3.py"：用于分析从FED3 SD卡导出的实验数据的代码，基于Python 3.11.4编写。该工具可将FED3原始数据转换为可由ClockLab打开的文本文件格式。