GOSH hardware grant readings

[jcahill]

Various miscellaneous readings for workup of GOSH hardware grant proposal.

Themes

• imaging, esp. fluorescence
• colony picking
• sterilization

Imaging

Details

µCube

• Info
  • framework
  • useful to keep in design toolbag
• Links
  • pub
    • http://doi.org/10.5334/joh.8
    • https://www.repository.cam.ac.uk/handle/1810/278797
  • src & doc
    • http://docubricks.com/projects/ucube
      • http://docubricks.com/viewer.jsp?id=4602764892958441472
    • https://github.com/mdelmans/uCube
      • https://mdelmans.github.io/uCube
    • https://hackster.io/delmans/ucameracube
    • https://hackster.io/delmans/ulightcube

BioARTS Microscope

• Info
  • 'facile' miniature microscope
  • claims assembly from off the shelf parts in under 10min
• Links
  • pub
    • https://doi.org/10.1371/journal.pone.0215114
    • https://doi.org/10.1371/journal.pone.0215114.s001
    • https://doi.org/10.1371/journal.pone.0215114.s002
  • src & doc
    • https://github.com/BioARTS-Lab/Miniature_Microscope

BBB

• Info
  • breadboard bricks for optical assemblies
• Links
  • pub
    • https://doi.org/10.1016/j.ohx.2021.e00182

FluoPi

• Links
  • pub
    • https://doi.org/10.1101/194324
    • https://doi.org/10.1371/journal.pone.0187163
    • https://osf.io/dy6p2
  • src & doc
    • https://docubricks.com/viewer.jsp?id=7449430440606889984
    • https://github.com/RudgeLab/FluoPi
    • https://github.com/RudgeLab/FluoPi/wiki

FlyPi

• Info
  • Chagas et al.
• Links
  • pub
    • https://doi.org/10.1371/journal.pbio.2002702
  • src & doc
    • https://github.com/amchagas/Flypi

Formlabs Lenses

• Info
  • 3d printed lenses
  • Uses formlabs-brand clear resin and Form 2 or Form 3 SLA printer
• Links
  • pub
    • https://formlabs.com/blog/creating-camera-lenses-with-stereolithography/
    • http://amosdudley.com/weblog/SLO-Camera
  • src & doc
    • https://pinshape.com/items/25871-3d-printed-slo-printed-lens-camera

Octopi and Squid

• Info
  • acronym gore
    • Octopi
      • Open configurable high-throughput imaging platform
      • for infectious disease diagnosis in the field
    • Squid
      • Simplifying Quantitative Imaging Development and Deployment
  • multiple projects and publications involved
  • prakash et al.
• Links
  • pub
    • https://doi.org/10.1101/684423
      • see intro's link roundup on smartphone-based microscopy
    • https://doi.org/10.1242/prelights.13197
      • ^brief commentary on preprint
  • src & doc
    • https://squid-imaging.org
    • software
      • https://github.com/hongquanli/octopi-research
      • https://github.com/prakashlab/octopi-driver-board
      • https://github.com/prakashlab/squid-tracking
    • More
      • https://squid-imaging.org/#:~:text=Assets

PiCamera color correction

• Info
  • characterise and correct the vignetting and colour crosstalk of Pi camera module v2
• Links
  • pub
    • http://doi.org/10.5334/joh.20
  • src & doc
    • https://gitlab.com/bath_open_instrumentation_group?sort=latest_activity_desc

Picroscope

• Links
  • pub
    • https://doi.org/10.1101/2021.05.17.443454
    • https://doi.org/10.1038/s42003-021-02779-7
  • src & doc
    • https://github.com/braingeneers/picroscope-supplement

PFIBox

• Links
  • pub
    • https://doi.org/10.1016/j.cels.2018.07.004
  • src & doc
    • https://github.com/sfrench007/pfibox

POLIR

• Info
  • Raspberry Pi Camera Open-Source Laboratory Imaging Robot
  • direct adaptation of 3d printer
• Links
  • pub
    • https://doi.org/10.1371/journal.pone.0224878
  • src & doc
    • https://reprap.org/wiki/CoreXY
    • https://gitlab.com/AlEdwards/polir

UC2

• Info
  • framework
• Links
  • pub
    • https://doi.org/10.1038/s41467-020-19447-9
  • src & doc
    • http://github.com/bionanoimaging/UC2-GIT
    • https://github.com/bionanoimaging/UC2-Software-GIT
    • GenericDeconv program for deconvolution is available upon request

Other

• Squid's linklist: https://squid-imaging.org/#:~:text=list%20of%20related%20work
• Eisenstein, M. Microscopy made to order. Nat Methods 18, 1277–1281 (2021). https://doi.org/10.1038/s41592-021-01313-1
• Fantner, G.E., Oates, A.C. Instruments of change for academic tool development. Nat. Phys. 17, 421–424 (2021). https://doi.org/10.1038/s41567-021-01221-3

Picking

The world of part-manipulating desktop robotics is quite diverse.
For our purposes, we are free to cherrypick ideas from:

1. Conventional pick and place (PnP) devices
2. Fused filament fabrication devices, i.e. 3D printers
3. Biodesign/prototyping devices oriented toward microfluidics, ex. opentrons

Our key questions will lie with balancing tradeoffs between

• build complexity (how 'involved' is this system to build and maintain?),
• build robustness (how's the build quality? can it damage other instruments?),
• build compactness (how well does the footprint satisfy spatial constraints?),
• task-generality (what can the system do beyond colony picking?), and
• BOM total as a fraction of project budgeting (how much can we spend on this?).

Sterilizing