Agar Microchamber Image Processing and Analysis

This repository contains code for processing images of diverse motile organisms, as well as code for analyzing confinement space for a range of organisms of different sizes. The processed images and analysis are included in the publication 'Gotta catch ‘em all: agar microchambers for high-throughput single cell live imaging'. Also, a detailed protocol for making the agar microchambers can be found on protocols.io. Molding microchambers in agar with PDMS stamps for live imaging.

Summary of Chlamydomonas smithii motility in agar microchamber

How to run

This repository has two independent parts:

• R analysis notebook (code/R/analysis.ipynb) predicts optimal chamber sizes from the publicly available BOSO-Micro dataset, which it downloads itself. It is intended to run on Google Colab and uses Unix shell commands (wget/unzip), so a Unix-like environment is required (the Windows workstation specs below describe the Fiji image-processing setup, not the R notebook). Open it directly in Colab:
• Fiji macros (code/Fiji/*.ijm) are interactive image-processing utilities run from Fiji (ImageJ2 2.9.0/1.53t). See code/Fiji/README.md for what each macro does. The microscopy images these macros operate on are published with the associated pub.

Versions and platforms

Fiji macro was used with ImageJ2 Version: 2.9.0/1.53t Build: a33148d777

Computation was performed on an image analysis workstation with the following specifications.

Operating system: Windows 10 Pro Version 21H2 OS Build 19044.1889

Platform | Intel Xeon C621E EATX Motherboard | Supermicro X12SPA-TF 64L CPU | Intel Xeon W-3365 2.7GHz Thirty-Two Core 48MB 270W | RAM | 8 x DDR4-3200 64GB ECC Reg. Video Card | NVIDIA RTX A6000 48GB PCI-E Primary Hard Drive | Samsung 980 Pro 2TB Gen4 M.2 SSD | Secondary Hard Drive | Samsung 870 EVO 4TB SATA3 2.5inch SSD | Tertiary Hard Drive | Western Digital Ultrastar 18TB SATA3 | Case | Fractal Design Define 7 XL Power Supply | Super Flower LEADEX Platinum 850W | Additional Cooling | Case Fans Upgrade Kit (PWM Ramping) |

Contributing

See how we recognize feedback and contributions on our code.