colosseum: open source fraction collector

A modular, highly customizable, open source fraction collector.

Tl;dr

We present colosseum, a low-cost, modular, and automated fluid sampling device for scalable microfluidic applications. The colosseum fraction collector can be built for around $100 using off-the-shelf components, and can be assembled in less than an hour. It uses 3D printed parts and common components that can be easily purchased from many retailers. The device can be run from a Windows, Mac, Linux, or Raspberry Pi computer with an easy-to-use GUI.

Table of Contents

1. What's included?
2. Getting Started
3. Setting up the hardware
4. Installing software
5. Startup checklist
6. Tips/Hints

What's included?

• Computer Aided Design (CAD) files of the 3D printed components.
• Controller software (Python) and a graphical user interface (GUI) to control the motor.
• Arduino firmware to send commands to the motors and receive commands from the GUI.
• Bill of materials for sourcing and purchasing materials (up to date as of 1/23/2023).
• Detailed assembly instructions of hardware components.
• Single click executable files for Mac, Windows, Linux, and Raspberry Pi systems.
• A web-based GUI you can run from Chrome without the need to install any Python packages.

Getting Started

What do I need to buy? The bill of materials with prices and vendor links is available on a Google Spreadsheet.

What do I need to make? The 3D printed components can be fabricated on any desktop fused filament fabrication (FFF) 3D printer. They were designed using Autodesk Fusion 360, a proprietary CAD software that offers free academic licenses. STL, STEP, IGES, Fusion 360 archive files, and bill of materials are available in the HARDWARE/ folder. They can be used with any slicing software to generate GCode for 3D printing. Here is a Fusion 360 view of colosseum:

Setting up the hardware

We have four 3D printed parts for colosseum, which are:

• tube rack
• base
• base plate (support needed)
• dispenser arm (support needed)

The print parameter for these parts are as follows:

• 1.75 mm diameter PLA filament
• nozzle temperature: 215°C
• bed temperature of 60°C
• 10% infill
• 0.2 mm layer height for slicing

Building colosseum

This video will guide you through the building process of colosseum.

There is also a step-by-step guide of the assembly.

Here are the steps for building colosseum:

1. 3D print components.
2. Attach set screws to the tube bed.
3. Insert small ball bearings into base.
4. Attach rubber feet on base.
5. Insert rotary shaft into base and fix in place with ball bearing.
6. Screw the stepper motor onto the base (with washers on the hex screws) and attach motor couplings.
7. Screw base plate onto base.
8. Insert ball bearings into the slots on base plate.
9. Insert another rotary shaft into arm and fix with set screw.
10. Insert torsion spring into base plate and arm.
11. Slide the tube bed through the center rotary shaft and align with arm.
12. Tighten all set screws and run!

Setting up the Arduino

We use the Arduino CNC shield to allow for up to three fraction collectors to be controlled from a computer.

The software is configured to run the stepper motors with 200 steps per revolution at 1/4 microstepping, which translates to 800 steps per rotation. To configure this, it is necessary to add a jumper between the M1 pin of the Arduino CNC shield. More information about microstepping can be found in the product page for the DRV8825 Stepper Motor Driver, which is used by the CNC shield.

The Arduino should be flashed with the motor_serial_com.ino sketch, available in the firmware/ folder.

Make sure to download and install the AccelStepper library. To install, unzip the zip file to the libraries sub-folder of your sketchbook.

The fraction collector is driven by an Arduino board that interprets commands sent via USB and sends the signals to control the stepper motor movement. For directions on how to flash an arduino please refer to the official guide: https://www.arduino.cc/en/Guide/HomePage

We recommend that you wrap wires in cable wraps and placing your Arduino+CNC shield in a case like this.

Installing software

You can run colosseum on Chrome by going to this link: https://pachterlab.github.io/colosseum/. Running colosseum on the browser platform will not require you to install any software.

To run colosseum locally, you can find the GUI script in the SOFTWARE/ folder. This GUI is used to interface with a Python script that controls the Arduino via USB.

The GUI is provided as a standalone Python package, installable with pip. To install the latest official release, open up the terminal and type:

pip install colosseum-ui

The Colosseum GUI is now installed and can be started by typing colosseum in the termnal. Before you run the system, MAKE SURE YOU HAVE INSTALLED THE ARDUINO FIRMWARE!!

Manual installation

You may also install the GUI manually by opening up the terminal inside the SOFTWARE/ folder and typing:

pip install .

If you get the following error when trying to run colosseum on Linux,

qt.qpa.plugin: Could not load the Qt platform plugin "xcb" in "" even though it was found.

you need to install the appropriate xcb library for your Linux distribution. For Ubuntu users, xcb can be installed with the following command:

sudo apt install libxcb-xinerama0

Startup Checklist

Before starting the Python controller, make sure

• The Arduino has the firmware uploaded to it
• The Arduino is connected via USB to the computer
• You have appropriately placed jumpers on the CNC Shield to allow for microstepping and hardware enabling (discussed in build video).
• The CNC shield is powered, and that all motors are plugged in to the CNC shield
• The dispenser arm is above the center of the first tube.

Tips/Hints

Things that we have learned along the way that may help with your build.

• The first tube can be used as a drip tube to catch any drips before you actually start collecting fractions. It will be numbered 0 on the GUI.
• If you hear a scratching noise while you rotate the tube rack, it means that the torsion spring on the arm is scratching the bottom of the tube rack so fold that end of the spring.
• If the dispenser arm does not rotate with the tube rack, it means that the follower on the arm is not correctly touching the grooves of the tube rack.
• Make sure to pull the motor away from the rotary shaft as much as possible so that the pulley belt is taut.

Safety Considerations

Please review the license before using/developing/distribution colosseum.

The colosseum fraction collector uses 3D printed PLA plastic and standard off the shelf components which do not pose a health hazard if handled correctly. Improper handling of plastics however can create hazards when working with organic solvents.

Before using the colosseum fraction collector in a wetlab environment, please ensure that you have thoroughly tested its functionality for your use case in a dry lab. Once the colosseum fraction collector has been moved into a wetlab, it should not be moved back to a drylab or dry workbench. If you plan to build on the colosseum fraction collector, ensure that you communicate any safety concerns that you may have with your design to potential users and collaborators.

If you want to contribute to colosseum, feel free to write on the Discussions page on this repo!