Cryo PiCam

Fast speed imaging of moving Cryo-EM specimens with time resolution. This project is inspired by the Vitrocam project and aims at using the lastest APIs for increased resolution and build an analysis toolbox for processing the images.

Hardware

ov9281 sensor
Raspberri Pi 4
add info about the motion sensor

Setting up the Raspberri Pi

Flash an SD card with RaspberriPi OS based on Debian Bullseye (32-bit)

Note: It should work with 64-bit but it has not been tested at this time.

Open /boot/config.txt and activate the kernel module for the ov9281 sensor.

sudo vim /boot/config.txt

#Add this line to the top of the file
dtoverlay=ov9281,media-controller=1

Update the repository and the installed packages
```
sudo apt update
sudo apt upgrade
```

Installation

Dependencies

install the system dependencies

sudo apt-get install build-essential cmake pkg-config libjpeg-dev libtiff5-dev libjasper-dev libpng-dev libavcodec-dev libavformat-dev libswscale-dev libv4l-dev libxvidcore-dev libx264-dev libfontconfig1-dev libcairo2-dev libgdk-pixbuf2.0-dev libpango1.0-dev libgtk2.0-dev libgtk-3-dev libatlas-base-dev gfortran libhdf5-dev libhdf5-serial-dev libhdf5-103 python3-pyqt5 python3-dev git -y

Other dependencies

sudo pip3 install pydantic matplotlib

## This one will take a while to build
sudo pip3 install opencv-python

Download CryoPiCam
```
git clone 
cd cryopicam
```
Edit your settings (more options soon)
```
vim settings.env

##Edit the values to your needs
dataDir=/home/pi/picam_data/
sensorPin=7
```
- dataDir: Where you want the data to be saved
- sensorPin: GPIO pin number where the motion sensor is connected on the pi.

Testing the installation

Coming soon

Usage

python run.py name_of_grid

It will create a grid_directory under the datadir and will save the raw stream as all_frames.raw of frames, the indiviual frames in frames/??.png, the timestamps with the frames as meta.json the timestamped movie as movie.mp4

The timestamps are relative to the sensor trigger timestamp. Negative number are frame prior to sensor activate and the positive numbers are from after.

JoQCcoz / CryoPicam