Data

Tools

Indexes

Applications

Experiments

Open Source Science

https://github.com/czbiohub-sf/ulc-malaria-scope

Instrument control software for the Remoscope project.

https://github.com/czbiohub-sf/ulc-malaria-scope

Science Score: 26.0%

This score indicates how likely this project is to be science-related based on various indicators:

  • ○
    CITATION.cff file
  • ✓
    codemeta.json file
    Found codemeta.json file
  • ✓
    .zenodo.json file
    Found .zenodo.json file
  • ○
    DOI references
  • ○
    Academic publication links
  • ○
    Academic email domains
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (11.8%) to scientific vocabulary
Last synced: 9 months ago · JSON representation

Repository

Instrument control software for the Remoscope project.

Basic Info
Statistics
  • Stars: 1
  • Watchers: 3
  • Forks: 1
  • Open Issues: 3
  • Releases: 20
Created almost 6 years ago · Last pushed 10 months ago
Metadata Files
Readme License

README.md

Remoscope: a label-free imaging cytometer for malaria diagnostics

An artistic rendition of the Remoscope

Introduction

This repository hosts instrument control software for the Remoscope, an automated and low-cost malaria diagnostic system, requiring minimal user training. The Remoscope was developed by the Bioengineering team at the Chan Zuckerberg Biohub San Francisco (CZBSF). The Remoscope images unstained fresh whole blood in liquid form and can screen up to two million red blood cells for Plasmodium falciparum parasites.

Please see our preprint here:

image

The Remoscope runs off a Raspberry Pi 4 Model B 8GB and an Intel Neural Compute Stick 2 (no longer available) to accelerate on-device neural network inferencing. The instrument control software is written in Python 3.7.3.

Repository structure

├── ulc_mm_package │   ├── utilities │   ├── summary_report │   ├── neural_nets │   ├── image_processing │   ├── hardware │   ├── configs │   ├── QtGUI │   ├── scope_constants.py ├── OS_instructions │   ├── OS_setup.md │   └── OS_flash.md ├── architecture_description ├── setup.py └── README.md

For a more detailed description of each folder and its scripts, see the architecture_description/ folder.

Installation and use

NOTE: If you are using a version downstream of commit 283a823 on develop (2024-03-06), you will need to install the stats_utils module. To do so, in the root directory run python3 -m pip install -e .

Option 1: Clone the image

  1. Flash a pre-existing image to an SD card (must be at least 32GB), see OS_flash.md

Option 2: Manual install

  1. Follow the instructions under OS_instructions.

Operation

To start the software, navigate to ulcmmpackage/QtGUI and run python3 oracle.py.

To use developer mode, navigate to ulcmmpackage/QtGUI and run python3 dev_run.py. This opens a GUI with manual hardware control for debugging purposes.

Related repositories

  1. Object detection - YOGO: https://github.com/czbiohub-sf/yogo
  2. Autofocus - SSAF: https://github.com/czbiohub-sf/ulc-malaria-autofocus
  3. Data processing utilities / model evaluations: https://github.com/czbiohub-sf/lfm-data-utilities/
  4. Statistics utilities: https://github.com/czbiohub-sf/remo-stats-utils

Owner

  • Name: Chan Zuckerberg Biohub San Francisco
  • Login: czbiohub-sf
  • Kind: organization
  • Location: San Francisco

GitHub Events

Total
  • Create event: 39
  • Release event: 7
  • Issues event: 2
  • Delete event: 35
  • Issue comment event: 6
  • Push event: 151
  • Public event: 1
  • Pull request review comment event: 21
  • Pull request review event: 40
  • Pull request event: 68
  • Fork event: 1
Last Year
  • Create event: 39
  • Release event: 7
  • Issues event: 2
  • Delete event: 35
  • Issue comment event: 6
  • Push event: 151
  • Public event: 1
  • Pull request review comment event: 21
  • Pull request review event: 40
  • Pull request event: 68
  • Fork event: 1

Issues and Pull Requests

Last synced: 10 months ago

All Time
  • Total issues: 2
  • Total pull requests: 38
  • Average time to close issues: over 1 year
  • Average time to close pull requests: 4 days
  • Total issue authors: 2
  • Total pull request authors: 4
  • Average comments per issue: 0.0
  • Average comments per pull request: 0.16
  • Merged pull requests: 25
  • Bot issues: 0
  • Bot pull requests: 1
Past Year
  • Issues: 1
  • Pull requests: 38
  • Average time to close issues: 8 months
  • Average time to close pull requests: 4 days
  • Issue authors: 1
  • Pull request authors: 4
  • Average comments per issue: 0.0
  • Average comments per pull request: 0.16
  • Merged pull requests: 25
  • Bot issues: 0
  • Bot pull requests: 1
View more stats
Top Authors
Issue Authors
  • paul-lebel (1)
  • i-jey (1)
Pull Request Authors
  • i-jey (32)
  • NicholasBratvold (1)
  • mwlkhoo (1)
  • dependabot[bot] (1)
Top Labels
Issue Labels
Pull Request Labels
dependencies (1) python (1)

Dependencies

.github/workflows/black.yml actions
  • actions/checkout v3 composite
  • actions/setup-python v4 composite
  • psf/black 23.1.0 composite
.github/workflows/type-checking.yml actions
  • actions/checkout v3 composite
  • actions/setup-python v4 composite
setup.py pypi
  • Jinja2 ==3.1.3
  • Pillow *
  • PyQt5 >=5.15.2
  • adafruit-circuitpython-mprls ==1.2.7
  • adafruit-circuitpython-pcf8523 ==1.5.5
  • adafruit-circuitpython-sht31d *
  • argparse *
  • matplotlib ==3.4.3
  • numba ==0.56.0
  • numpy ==1.21.0
  • opencv-python *
  • pigpio ==1.78
  • pimoroni-ioexpander *
  • py_cameras *
  • pymotors *
  • pypylon ==1.7.2
  • qimage2ndarray ==1.9.0
  • stats_utils *
  • tqdm ==4.63.0
  • transitions ==0.8.11
  • typer ==0.4.1
  • xhtml2pdf ==0.2.11
  • zarr ==2.10.1