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Benedict Diederich beniroquai

  • IPHT Leibniz Institute of Photonic Technology's
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beniroquai /
Last active February 7, 2024 14:20
Micro Plaque Essay using Autonomous Microscopy, Robots and Liquid Handling

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.


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


beniroquai / gist:3ef6f270e164d5a74ecdfb0dd71ee710
Last active January 9, 2024 15:32
setup ROS on mac in python
curl -L -O "$(uname)-$(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
beniroquai /
Last active October 7, 2023 15:14
Using ROS for a Microscope Farm: Overview

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.
import os
import re
import tifffile
# adjust to dataset:
input_dir = "PATH_TO_TIFFS"
pixel_size = 0.225
maximum_shift_microns = 50
beniroquai / gist:775ece6eadc5d831b10fcb91f1e9d61c
Created February 25, 2021 07:04
Install MicroManager on a Nvidia Jetson
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
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
exif_data = {}
<docs lang="markdown">
[TODO: write documentation for this plugin.]
<config lang="json">
"name": "UC2-Streamer",
"type": "window",
"tags": [],
"ui": "",
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