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Title: Automated Protocol for Phage Detection and Analysis

Objective: To detect and analyze bacteriophages using a combination of automated pipetting, robotic handling, microscopy, and image processing.

Equipment:

1. 96 Well scanning microscope (openUC2 FiveD)
2. Pipetting robots (Opentrons OT2)
3. Transfering Robot Arm (Dorna 2)

Reagents:

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curl -L -O "https://github.com/conda-forge/miniforge/releases/latest/download/Miniforge3-$(uname)-$(uname -m).sh"

bash Miniforge3-$(uname)-$(uname -m).sh

cd ~/mambaforge

mamba create -n ros_env
mamba activate ros_env

# this adds the conda-forge channel to the new created environment configuration 

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1. XYZ Stage Control:

• ROS Nodes: Create ROS nodes for each microscope that can control the XYZ stages and possibly other controls such as light intensity, filters, etc.
• MoveIt: Consider using MoveIt, a ROS plugin for motion planning. You could model the XYZ stages and utilize MoveIt to plan and execute motions.

2. Remote Operation:

• ROS Web Tools: Utilize ROS web tools to create a web interface that can communicate with ROS nodes. ROSBridge can be particularly useful for transmitting ROS messages over WebSocket.
• GUI: Design a graphical user interface on the web platform where you can visualize the status of each microscope and control them remotely.

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import os
import re

import tifffile

# adjust to dataset:
input_dir = "PATH_TO_TIFFS"
pixel_size = 0.225
maximum_shift_microns = 50

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On extrnal drive on Windows

Format sd card as NTFS
open powershell in this drive
shift right click
open powershell here


# Instal dependencies
# Here you have debian packages you can install with sudo apt-get install

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from __future__ import print_function
import PIL.Image
import PIL.ExifTags
import sys
import os

def formatted_exif_data(image):
    """Retrieve an image's EXIF data and return as a dictionary with string keys"""
    # with thanks to https://stackoverflow.com/questions/4764932/in-python-how-do-i-read-the-exif-data-for-an-image
    exif_data = {}

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<docs lang="markdown">
[TODO: write documentation for this plugin.]
</docs>

<config lang="json">
{
  "name": "UC2-Streamer",
  "type": "window",
  "tags": [],
  "ui": "",

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