Automated Drosophila embryo microinjection

An Automated microinjection platform for Drosophila embryos

Hardware Requirements

Computer
Arduino Nano
Custom built incline microscopes
XYZ stage
DSLR camera
Air prssure line
Electric pressure regulator

Software Requirements

The following libraries are used in the Autoinjector software (see install instructions for how to install).

Ananconda 3
Microsoft Visual C++ 2019 Redistributable and Microsoft Build Tools 2019
NVIDIA driver
CUDA
cUDNN
DigiCamControl
Arduino
Packages
- pip
- Native python libraties
  - time
  - sys
  - os
  - user
- tensorflow-gpu==2.10.0
- numpy==1.21.1
- opencv-python==4.5.5.62
- multiprocess
- tk
- pyserial

Install Instructions

Install the following software to operate the Autoinjector. It is recommended to install the software in the order it is listed. Make sure to run every file as administrator (right click, "Run as administrator")! Otherwise, the install may fail.

1. Anaconda

Download Anaconda3-2021.11-Windows-x86_64.exe here.
Launch the installer and follow installation instructions on screen.

2. Microsoft Visual

Download Microsoft Visual here.
Launch the installer and follow installation instructions on screen.

3. NVIDIA driver

Download the NVIDIA driver here.
Launch the installer and follow installation instructions on screen.

4. CUDA

Check which version of CUDA you need based on the tensorflow version required here
Download CUDA here.
Launch the installer and follow installation instructions on screen.

5. cUDNN

Check which version of cUDNN you need based on the tensorflow version required here
Download cUDNN here.
Follow these steps to install here.

6. DigiCamControl

Download the DigiCamControl here.
Launch the installer and follow installation instructions on screen.
Make sure an SD card is in the DSLR

7. Arduino

Download the DigiCamControl here.
Launch the installer and follow installation instructions on screen.
Upload AmeyArduinoCode.ino

8. Packages

Search Anaconda Prompt in the Windows search Bar. Open it, run as administrator, and run the following commands:

Tensorflow
```
pip install tensorflow-gpu==2.10.0
```
Numpy
```
pip install numpy==1.21.1
```
OpenCV
```
pip install opencv-python==4.5.5.62
```
Multiprocess
```
pip install multiprocess
```
Tkinter
```
pip install tk
```
Pyserial
```
pip install pyserial
```

Running the Application

To run the program, click the file "Robot_GUI_multipipette.py" in the Autoinjector folder. This will launch the GUI. For additional operating instructions see the user manual here.

License

This work is lisenced under the University of Minnesota lisence.

Name		Name	Last commit message	Last commit date
Latest commit History 11 Commits
DSLR_Camera		DSLR_Camera
ML		ML
Pressure_Control		Pressure_Control
XYZ_Stage		XYZ_Stage
__pycache__		__pycache__
Delta_XY_FOV_1_lin.py		Delta_XY_FOV_1_lin.py
Delta_XY_FOV_2_lin.py		Delta_XY_FOV_2_lin.py
Delta_Z_FOV_1_lin.py		Delta_Z_FOV_1_lin.py
Delta_Z_FOV_2_lin.py		Delta_Z_FOV_2_lin.py
Delta_px_y_FOV_1.py		Delta_px_y_FOV_1.py
Delta_px_y_FOV_2.py		Delta_px_y_FOV_2.py
GUI.py		GUI.py
Main_Code_25.py		Main_Code_25.py
Main_Code_25_automated.py		Main_Code_25_automated.py
Main_Code_25_automated_old.py		Main_Code_25_automated_old.py
Main_Code_25_automated_robo_1.py		Main_Code_25_automated_robo_1.py
Main_Code_25_automated_robot_1.py		Main_Code_25_automated_robot_1.py
Main_Code_25_sweep.py		Main_Code_25_sweep.py
Main_code_function.py		Main_code_function.py
Main_code_function_multi_pipette.py		Main_code_function_multi_pipette.py
README.md		README.md
Robot_GUI.py		Robot_GUI.py
Robot_GUI_multi_pipette.py		Robot_GUI_multi_pipette.py
Running the robot.pdf		Running the robot.pdf
Stream_code_function.py		Stream_code_function.py
Two_Cameras_NEW.py		Two_Cameras_NEW.py
Two_Cameras_NEW_NEW.py		Two_Cameras_NEW_NEW.py
accelerate_pressure.py		accelerate_pressure.py
barcoding_analysis.py		barcoding_analysis.py
barcoding_plotting_script.py		barcoding_plotting_script.py
client.py		client.py
currentXY.npy		currentXY.npy
decelerate_pressure.py		decelerate_pressure.py
detect_injection.py		detect_injection.py
find_posterior_new.py		find_posterior_new.py
first_pipette.py		first_pipette.py
go_to_position.py		go_to_position.py
go_to_position_new.py		go_to_position_new.py
injection_ml_tip_short_centroid_new.py		injection_ml_tip_short_centroid_new.py
injection_ml_tip_short_centroid_new_old.py		injection_ml_tip_short_centroid_new_old.py
injection_ml_tip_short_new.py		injection_ml_tip_short_new.py
injection_ml_tip_short_new_thresh.py		injection_ml_tip_short_new_thresh.py
injection_results.py		injection_results.py
injection_results_new.py		injection_results_new.py
most_optimal_path.py		most_optimal_path.py
move_embryo_fov_new_new.py		move_embryo_fov_new_new.py
move_embryo_fov_new_new_thresh.py		move_embryo_fov_new_new_thresh.py
move_embryo_fov_new_new_thresh_pressure.py		move_embryo_fov_new_new_thresh_pressure.py
move_embryo_fov_new_new_thresh_pressure_robot_1.py		move_embryo_fov_new_new_thresh_pressure_robot_1.py
move_embryo_fov_new_new_thresh_pressureold.py		move_embryo_fov_new_new_thresh_pressureold.py
new_pipette_new.py		new_pipette_new.py
new_z.py		new_z.py
path_finder_new.py		path_finder_new.py
point_and_click.py		point_and_click.py
pressure_calc.py		pressure_calc.py
stop.py		stop.py
stream.py		stream.py
stream_function_multi_process.py		stream_function_multi_process.py
stream_image.py		stream_image.py
stream_image_old.py		stream_image_old.py
stream_new.py		stream_new.py
stream_old.py		stream_old.py
testing_stream_and_pressure.py		testing_stream_and_pressure.py

bsbrl/Automated-Drosophila-embryo-microinjection

Folders and files

Latest commit

History

Repository files navigation