Incubicles

Incubator Modules for the Home Bio Lab

Abstract

Home DIY Bio Labs have become commonplace, basic DIY Bio Hardware and Tools can be made in FabLab or sourced on the second-hand market.

Biological experiments often require environmental controls, usually laboratory incubators are fridge-sized appliances, incubators are usually set at at target temperature. The size of laboratory incubators make them impractical for a home setup, requiring both a high space and energy commitment. Maintaining a range of incubators with different temperatures in a Home Lab environment is therefore not practical.

This project proposes small, configurable, networked incubator modules that can be configured for a range of Home Lab requirements. Existing home infrastructure like lightening rails and existing shelving systems are used to integrated and blend the incubators into the home environment.

Monitoring and Control of the incubators is done through a dedicated website/app.

Motivation

Doing DIY Bio at home is becoming both feasibly and necessary, as lab access to universities and bio-hacker spaces can be affected by restrictions and lockdown.

DIY Bio tools and equipment, like PCR machines, Clean-benches, Centrifuges, Microscopes can either be made DIY style or bought through second-hand. See Bento Bio, Amino Labs, etc for low-cost lab equipment and Hackteria, BioHack Academy, GoSH, etc for open source lab devices and tools.

While mini incubators can had for around ¥10,000 ($100), they are too big and don't have networking and observation capabilities.

My project is to make small incubators for DIY bio experiments, that blend and fit into the home.

• Small Size, Capacity, between 1 - 10 standard petri dishes.
• Integrate seamlessly into home environment
• Multiples
• Take advantage of temperate variations within rooms (top hotter, bottom cooler)
• Move Incubators vertically for optimal temperature
• Network devices for remote observation

Questions

• Peltier Device for Heating/Cooling? Alternatives?
• Temperature Sensors? How to make them Water-proof? Coat with PDMS?
• How to move vertically? Worm-gear?

Extensions

• C02 Incubator for Mammalian Cells? Which CO2 Source in a Home Setting? Food Cartridges? SodaStream, iSi Soda Cartridge?

Spiraling & Scaling

An incubator is quite a common and basic tool for working and collaborating with micro-organisms. I choose it, because:

• I found myself in situations I could not keep micro-organisms and plants alive, because of the lack of suitable incubator
• It it spiralable and scalable.

Spiraling Opportunities

• Temperature Control
• Light Control
• Camera, Visual Monitoring
• Data Logging, WiFi, Monitoring/Controlling via Internet
• Scale of Incubator (Nano, Micro Incubators?)
• Feeding Mechanism
• Turbidity Sensing
• CO₂ Control

Background

Climate in Japan

The climate in around Tokyo and Kamakura is not a extreme as in the north, winters can get below 0ºC, summers can be around 40ºC - with high levels of humidity. Houses are following strict earthquake-proofing regulations, mostly fabricated from wood, not much isolation - I assume because of the humidity, and its effect on isolation material. Heating cooling is done with air-conditioners, which have the disadvantage, that as soon as you turn them off, the inside temperature aligns with the outside temperature rather quickly.

Access to Incubators and DIY Bio/BioHacking

Access to incubators in universities and bio-hackers spaces can be difficult during the pandemic. A range of tools, equipment and tactics for and from the BioHacking community exists:

• DIY approaches to Magnetic Stirrers, DIY PCR Machines, Centrifuges, etc
• Affordable Lab equipment like the Bento Lab or Amino Labs
• Second-hand Lab Equipment

Cheap, affordable Incubators are also on the market, cheap ones can be had for ca ~¥10,000 (~$100, ~€85), giving you a basic temperature-controllable environment.

Sometimes these cheap, affordable options are not suitable, after all, it depends on the collaborating organism - and which environment, or milieu, it needs.

Organisms have their own specific environments, here are some common - and more extreme - examples.

• 37ºC, 5% CO₂
• 24ºC, Photo-period of 16h
• 1ºC, High Humidity
• ...

The Incubator(s)

While I am very clear on the functionality of the incubator, I am less clear about the shape and form of it. Most incubators have fridge-like designs - which take up a lot of space - I would like to explore possible design and sizes.

• Picture Frame Incubator
  Hang your incubator on the wall.

• (Muji) Shelf Incubator
  Incubator that fits in standard Muji Shelves. 340mm x 340mm x 275mm.

• Mini/Micro Incubators
  How small can the incubator be? Smaller Incubators can scale in number, which in turn enables parallel parameter search for the most suitable growing parameters.

• Parasite/Parasitic Incubators
  Repurpose and re-function already existing boxes and containers. Natural incubators situations within the house/room.

• Suspended Ceiling Incubators
  Use a common light rail, and 100V supply to suspend micro-incubators from the ceiling. Use distance sensors and work-gear-motor(?) to vertically move the micro-incubators to hotter or colder zones within the room.

Planned Technical Setup

• ESP32
• Peltier Device for Heating/Cooling
• Laser ToF for Distance Sensing Top/Bottom
• Temperature Sensors (Onewire) for measuring inside/outside
• Double Wall for Isolation
• Light Source for Plants/Photosynthesis

Incubator for Sea Sparkle?

• Make an incubator* for N. scintillans (Sea Sparkle, ヤコウチュウ, 夜光虫)
• Catch N. scintillans at Kamakura's Yuigahama Beach
• Grow and multiply N. scintillans in the incubator
• Mechanically and selectively agitate/excite the water and N. scintillans
• Create a volumetric bioluminescence display

Catching N. scintillans at Yuigahama Beach in Kamakura

The FabLab Kamakura is about 500m from the beach, that's where I observed (for the first time) the amazing and magically spectacle of glowing Sea Sparkle. The picture above was taken in May. Need to observe the most suitable weather conditions of the last blooms and find suitable weather forecasts for upcoming blooms. (Side Project: Make Forecast Site for Sea Sparkle Bloom, can it be seen from satellites?)

Growing N. scintillans

Sea Sparkle grow in Artificial Seawater Medium, with Guillard's (F/2) Marine Water Enrichment Solution, which is for growing Micro-algae, which in turn are consumed by N. scintillans. Suitable temperature are from ca. 10ºC - 24ºC, N. scintillans also has a funky diplontic life cycle, the incubator(s) can also help in finding the right growth conditions for the different life cycle stage.

Many Opportunities for Failing

Ok, now we are getting to the really interesting part. I am aware that this is quite a large and long project, with one big uncontrollable parameters (what if there is no Sea Sparkle bloom in Kamakura this year?) I could try to obtain Sea Sparkle from other sources, but I like the fact that the beach with the organisms and the FabLab are in close, hyper-local distance. Even if I can not obtain and grow the Sea Sparkle, the incubator will functioning and ready. Which is a also a success in itself.

Volumetric Bioluminescence Display

In the best-case scenario, I have the Sea Sparkle, they are growing abundantly, we are now ready for the final experiments. Mechanically disturbing a container of Sea Sparkle light up the container. How can we selectively excise the Sea Sparkle? How can we selectively shake the water? Transparent Nylon wires? Ultra-sound? What is the exact activation energy that Sea Sparkle need to bioluminescent? These questions and experiments can only be done once we can stably and reliably grow and cultivate the organisms.

Schematic Sketches

UI Sketch

Pre-Visualisation

Ceiling Lights

Ceiling Lights (天井照明) in Japan 100V, 50Hz in Eastern Japan, 60Hz in Western Japan - depending from where the first power stations got imported back in the day. The need to care for both 50Hz and 60Hz for the national market might also be a reason, why Japan was so successful in exporting their electronic products to different foreign markets. (Analog TVs relied on the frequency to sync their image. That's why PAL was 50Hz, and NTSC 60Hz, and that's why we still have these frame rates in modern cameras.)

Lighting Rails

Lighting rails are systems for mounting one or more lights (or power adaptors) on a rail usually suspended from the ceiling. Lighting rails allow for the flexible and individual position of lights, and with their integrated mechanical and electrical connector they make it easier to place multiple lights.

Universal Ceiling Sockets in Japan

Japanese houses and apartments are equipped with universal, non-grounded twist lock sockets, which not only provider power but also allow for the suspension of lamp shades etc.

• https://www.monotaro.com/g/00268249/
• https://www.monotaro.com/p/4105/3896/

The socket can support up to 5kg and up to 10kg if a hook is used to distribute the weight.

Provisional Bill-of-Materials

Electroncics Vendors in Japan

Offline AND Online, (all Akihabara):

• https://akizukidenshi.com
• https://www.sengoku.co.jp
• https://www.aitendo.com

Online only:

• https://www.switch-science.com
• https://www.digikey.jp
• https://www.mouser.jp-
• https://www.robotshop.com/jp/en/

Bill of Materials

Possible Modules

• Temperature Module
• Lightening Rail Suspension Module
• Light Socket Suspension Module
• CO₂ / Temperature Module
• Growth Light Module
• Growth Light & Camera Module
• UV Light Module

Module Configurations

Why the need for independent modules? Why not integrate everything into one system? Incubators haves different requirements, depending on the use-case. To allow for a

Example 1: Suspended Incubator with Room Temperature Adjustment

• Incubator Module x2
• Suspension Module
• Payload: Petri dishes x10
• Target Temperature: 25ºC
• Organism: xxx

Example 2: Shelf Incubator

Use existing shelf infrastructure (Muji, Ikea, etc) for incubation.

• Incubator Module
• Payload: Petri dishes x40
• Target Temperature: 25ºC
• Organism: xxx

Biopolar Stepping Motor Driver: https://akizukidenshi.com/catalog/g/gI-07408/

https://maker.pro/custom/tutorial/how-to-select-the-best-motor-driver-for-your-project

https://www.digikey.jp/product-detail/en/rohm-semiconductor/BD6222HFP-TR/BD6222HFPTR-ND/1936306

Fan Controller

https://pdfserv.maximintegrated.com/en/ds/MAX31790.pdf

6-Channel PWM-Output Fan RPM Controller, I2C

Peltier Drivers

I am still confused about how to efficiently drive a Peltier Device. There seem to be 3 choices:

• PWM
• Class D Audio Amplifiers
• Dedicated Peltier Driver

PWM - Bad or not?

Using PWM to drive a Peltier works, but it is not efficient and will decreased the life-span of the device.

https://electronics.stackexchange.com/questions/118536/thermistor-control-of-peltier-voltage-with-arduino-for-dslr-chill-box-project

https://forum.allaboutcircuits.com/threads/driving-a-peltier-with-power-op-amp-pi-control.138587/

Class D Audio Amplifiers for driving Peltier

https://www.infineon.com/dgdl/an-1071.pdf?fileId=5546d462533600a40153559538eb0ff1 https://www.ti.com/lit/an/snaa092/snaa092.pdf

Dedicated Peltier Driver

• MAX1968 ~¥1,700

• LTC1923 High Efficiency Thermoelectric Cooler Controller, ~¥3,500

Application Reports

• Power Drivers for Peltier TEC Modules
• How to Control and Compensate a Thermoelectric Cooler
• TI SLVA677–December 2014: Low-Power TEC Driver
• Designing a High Performance TEC Controller

Buck-Booster Converter?

Examples from FabAcademy Archive

Nciri Mejdi:

...high-current DC motor driver + a low-pass LC filter... http://archive.fabacademy.org/2018/labs/fablabdigiscope/students/nciri-mejdi/Final_Project.html

Tomasero:

Therefore, I had to implement a low-pass filter to keep the instantaneous current closer to the average current. However, I didn't want to add more hardware, so he suggested decreasing the PWM frequency to a low range of 1 to 100Hz https://fab.cba.mit.edu/classes/863.17/CBA/people/tomasero/

Daisuke Doyo:

... using SSR to drive Cartridge Heater http://archive.fabacademy.org/2018/labs/fablabkamakura/students/daisuke-doyo/assignments/week12.html

Driving the Peltier

After some discussion and advice from both the Global Open Time Sessions and from our local electronics guru Yamamoto-san, BD6231F-E2

Power Supply & H-Bridges

Settled on using a DC-DC Convertor board to supply power to the project

• Input 12V

• PWM 12V to Fan

• PWN 6V to Peltier

• Step down to 3.3V to power ESP32

• A4953 to drive Fan with 12V. The A4953 needs VBB from 8-40V

• BD6231F-E2 to drive Peltier with 6V.

Ceiling Modules

• Suspend Ceiling Module
• Which Stepper Motor?
• Which Driver?
• Shaft-mount winding disc?
• Which suspension wire? Fish Line?
• Ball-bearing for Stepper Motor Shaft to distribute weight?
• Power Adapter? How much for downstream Peltier devices?

Temperature Modules

• remove excess heat from cooling Peltier? Fan? Sink? Both?
• PWM for Peltier Devices.

Task List

List of atomic tasks. Task go into the schedule.

Module

Module Designs

3D Printing Module

Starting a (small) Print Farm

First Print Results: Printing Time: 7h 06m

Improvements for next prints:

• Bigger Holes for Connecting Screws
• Space for Power Button

Side Connectors

Side Connectors and Tests

Door Connectors

One thing I nearly forgot, when getting carried away with the modular aspects of the design - is a door:

Test Assemble of Suspension Module

Top and Bottom Housing, and Side Connectors are 3D printed, the Side Walls and Cable Channel Covers and Module Covers are laser-cut.

Gram & Lasercutting

A last week Global Open Time session Leo McElroy was presenting his amazing Gram Language. Gram is parametric line drawings language for digital fabrication technologies like laser cutters and CNC mills.

h = 109
w = h
r = 10
hole = 4/2

square = layer:
  newstroke [r 0]
  for 2:
    forward h-r*2
    arc 90 r
    forward w-r*2
    arc 90 r

fixtures = layer:
  layer:
    circle hole
    translate 25 5
  layer: 
    circle hole
    translate 5 25
  copypaste n = 4:    
    rotate [h/2 h/2] 360/(n)

x = 7
dist = 5
airholes = layer:
  for x as i:
    for x as j:
      layer:
        circle 2 - i*0.1 -  j*0.1
        translate h/2 + 10 + dist*i w/2 + 10 + dist*j

OK, it's not a heroic program, it does not do anything unexpected, but what it does, it does very well.

• A square cover with rounded edges
• Holes for fixing the cover to the module
• Air holes for the Peltier/Fan exhaust air

Saving as SVG and importing to Inkscape to prepare for laser cutting went without drama.

https://leomcelroy.com/gram/?code=㐐཈ئΐ厹ô䃐ੲ抇ʚ෭䙒ǩÐ幤ਊ㦸嵘⹘䃦挋斕摴ਠ့ᥝ湮䜦筛ᒁ㛤‰⺅ࠈ್眢Ɩၯਖ睡㤲ࠚ֮⊣ᘨ䦅擆‹᠐Ჳ⏮絁硓ᦥ烨畲㊹猛夡ሂ̛◉䛘攠爀➱∎䜦୳䶱䋨攠ᤚ䠍㤥䈍祩咀斈ⵣ㞸Ṝమ㝆⤃㮐ǘ㫄ዢ䪜䷮䱂㫛₼摀栯᤮䠌曆˲䍱➐ń砠Ẑෂ䲍᜷℁璀樔慩㥢᡻‖Ṁ࡫悁䋦⁩璀䒱䈍ⱡݨ͏嘁⨲ဖ䠚╆ˣँ㒀䃕䐉撑㪀វ䀉⅙Ä恀⬠爀⅊䴤ݼ碓⬤气 耀

Laser-cutting

Circuit Board Design

Logic Board

• ESP32
• WiFi Communication
• I2C Bus to ToF and OLED
• 1-Wire Bus to Temperature Sensors
• FX230 for USB/Serial Communication
• 3.3V Voltage Regulator

JST Connector Zoo

I want to make the connections to sensors and boards clean and flexible, the different-sized JST connectors let themselves to different connective functions.

• Power: XH 2 Pin
• Fan, Pelter: PH 2 Pin
• 1-Wire: ZH 3 Pin
• I2C: ZH 4 Pin

JST Eagle Libraries

JST is the name of the company, the different names (XH, PH, ZH, etc) describe a range of standards. Because of the variety of the connectors, it can be both confusing and difficult to find working and correct libraries for Eagle.

Searching for JST on eagle.autodesk.com shows a number of results. These are working for me:

ZH (Library Name: jst.lbr)
http://eagle.autodesk.com/eagle/download/505

XH (Library Name: jst_xh_connectors_v1-0.zip )
http://eagle.autodesk.com/eagle/download/51

I could not get the PH Library from the Eagle site to show up in Eagle, but I found an alternative one here:

PH (Library Name: con-jst-ph.lbr)
https://github.com/robertstarr/lbr_user/blob/master/con-jst-ph.lbr

Adventures in Crimping

• Crimping XH
• Crimping PH
• Crimping ZH

Board Milling Images

Boards

System Integration

License

Incubicles is shared under the Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0) license.

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