luminos-microscopy

Bi-directional microscopy software

https://github.com/adamcohenlab/luminos-microscopy

Science Score: 52.0%

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

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CITATION.cff file
Found CITATION.cff file
✓
codemeta.json file
Found codemeta.json file
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.zenodo.json file
Found .zenodo.json file
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DOI references
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Academic publication links
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Academic email domains
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Institutional organization owner
Organization adamcohenlab has institutional domain (cohenweb.rc.fas.harvard.edu)
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JOSS paper metadata
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Scientific vocabulary similarity
Low similarity (8.2%) to scientific vocabulary

Last synced: 6 months ago · JSON representation ·

Repository

Bi-directional microscopy software

Basic Info

Host: GitHub
Owner: adamcohenlab
License: other
Language: PostScript
Default Branch: main
Homepage: https://luminosmicroscopy.com
Size: 23.7 MB

Statistics

Stars: 6
Watchers: 10
Forks: 0
Open Issues: 2
Releases: 3

Created over 2 years ago · Last pushed about 1 year ago

Metadata Files

Readme License Citation

README.md

Luminos is a MATLAB library for bi-directional microscopy: simultaneous high-speed imaging and patterned optical stimulation.

Documentation

You can find the Luminos documentation on the website. Check out the Getting Started page to get set up.

New features in v0.4 (Updated 2/14/25):

Improved DMD calibration using AprilTags, select between different patterns and transforms
Calibrations fully agnostic to ROI or Binning
Rotate or Flip Camera FOV
Camera ROI option centered with offset (define midpoint and height/width)
Real time pixel brightness histogram and optional histogram equalization
Multi-Round acquisition and meta-experiments (for Standard acquisition, Snaps, Waveform only, Hadamard or HiLo)
Autofocus using motorized z-stage or xyz-stage
Automated setup of z-stacks, multiwell plate acquisitions etc. in GUI, compatible with autosampler
ROI brightness plotter support for multiple cameras
Distance measurements in live stream and DMD circle drawing in pixels or absolute units (um,mm,cm)
Button for aborting running acquisition
Toggle for blanking screen during acquisition
Flexible trigger setup using non-PFI DO, PFI-DO or CTR
New User Manual on Luminos Website

New features in v0.2 (Update 6/13/24):

Support for Teledyne Kinetix camera
Automated DMD calibration using AprilTags
Support for Newport motor controller
Acquisition triggerable by external TTL pulses
Acquisition with cameras without clock output
Digital confocal setup using Hadamard and HiLo
Automated SLM Calibration
Improved functionality of scanning devices
Fixed lots of bugs

Owner

Name: Cohen Lab
Login: adamcohenlab
Kind: organization
Location: Harvard

Website: http://cohenweb.rc.fas.harvard.edu/
Repositories: 1
Profile: https://github.com/adamcohenlab

Citation (CITATION.cff)

# This CITATION.cff file was generated with cffinit.
# Visit https://bit.ly/cffinit to generate yours today!

cff-version: 1.2.0
title: Luminos
message: >-
  If you use this software, please cite it using the
  metadata from this file.
type: software
authors:
  - given-names: Hunter C.
    family-names: Davis
    affiliation: Harvard University
  - given-names: F. Phil
    family-names: Brooks
    name-suffix: III
    affiliation: Harvard University
    orcid: "https://orcid.org/0000-0002-4334-8192"
  - given-names: Raphael
    family-names: Hotter
    affiliation: Harvard University
  - given-names: Daniel G.
    family-names: Itkis
    affiliation: Harvard University
  - given-names: Marley
    family-names: Xiong
    affiliation: Harvard University
  - given-names: David
    family-names: Wong-Campos
    affiliation: Harvard University
  - given-names: "Rebecca "
    family-names: Frank Hayward
    affiliation: Harvard University
  - given-names: Bill
    family-names: Jia
    affiliation: Harvard University
  - given-names: Madeleine
    family-names: Howell
    affiliation: Harvard University
  - given-names: Byung Hun
    family-names: Lee
    affiliation: Harvard University
  - given-names: Adam E.
    family-names: Cohen
    email: cohen@chemistry.harvard.edu
    affiliation: Harvard University
    orcid: "https://orcid.org/0000-0002-8699-2404"
repository-code: "https://github.com/adamcohenlab/luminos-microscopy/"
url: "https://www.luminosmicroscopy.com/"
abstract: >-
  To make optical electrophysiology more generally
  accessible, we present Luminos, an open source

  library for highly synchronized microscope control. While
  motivated by the demands of

  optical elecrophysiology, this library is general and is
  intended to be used for a wide range of experiments. This
  library combines support for high-speed camera acquisition
  and highly synchronized digital and analog I/O for control
  of custom microscopy rigs.
keywords:
  - Microscopy
  - Automation
  - Synchronized
  - Camera
  - Scanning
  - Patterning
  - Optical physiology
  - Voltage imaging
  - Software

version: v0.2
date-released: "2024-06-13"

GitHub Events

Total

Create event: 1
Issues event: 1
Release event: 1
Watch event: 4
Issue comment event: 4
Push event: 1

Last Year

Create event: 1
Issues event: 1
Release event: 1
Watch event: 4
Issue comment event: 4
Push event: 1

Dependencies

src/User_Interface/frontend/package.json npm

@tailwindcss/typography ^0.5.8 development
@vitejs/plugin-react ^4.0.0 development
autoprefixer ^10.4.13 development
postcss ^8.4.19 development
tailwindcss ^3.2.4 development
vite ^4.3.9 development
@emotion/react ^11.11.1
@emotion/styled ^11.11.0
@headlessui/react ^1.7.4
@heroicons/react ^2.0.13
@mui/material ^5.11.0
@tailwindcss/forms ^0.5.3
classnames ^2.3.2
lodash ^4.17.21
notistack ^2.0.8
react ^18.2.0
react-dom ^18.2.0
socket.io-client ^4.5.4
styled-components ^5.3.6
tailwind-merge ^1.8.1
uplot ^1.6.23

src/User_Interface/relay/package.json npm

express ^4.18.2
socket.io ^4.5.4

src/User_Interface/frontend/package-lock.json npm

244 dependencies

src/User_Interface/relay/package-lock.json npm

@socket.io/component-emitter 3.1.0
@types/cookie 0.4.1
@types/cors 2.8.17
@types/node 20.10.5
accepts 1.3.8
array-flatten 1.1.1
base64id 2.0.0
body-parser 1.20.2
bytes 3.1.2
call-bind 1.0.7
content-disposition 0.5.4
content-type 1.0.5
cookie 0.6.0
cookie 0.4.2
cookie-signature 1.0.6
cors 2.8.5
debug 2.6.9
debug 4.3.4
define-data-property 1.1.4
depd 2.0.0
destroy 1.2.0
ee-first 1.1.1
encodeurl 1.0.2
engine.io 6.5.4
engine.io-parser 5.2.1
es-define-property 1.0.0
es-errors 1.3.0
escape-html 1.0.3
etag 1.8.1
express 4.19.2
finalhandler 1.2.0
forwarded 0.2.0
fresh 0.5.2
function-bind 1.1.2
get-intrinsic 1.2.4
gopd 1.0.1
has-property-descriptors 1.0.2
has-proto 1.0.3
has-symbols 1.0.3
hasown 2.0.2
http-errors 2.0.0
iconv-lite 0.4.24
inherits 2.0.4
ipaddr.js 1.9.1
media-typer 0.3.0
merge-descriptors 1.0.1
methods 1.1.2
mime 1.6.0
mime-db 1.52.0
mime-types 2.1.35
ms 2.1.2
ms 2.0.0
ms 2.1.3
negotiator 0.6.3
object-assign 4.1.1
object-inspect 1.13.1
on-finished 2.4.1
parseurl 1.3.3
path-to-regexp 0.1.7
proxy-addr 2.0.7
qs 6.11.0
range-parser 1.2.1
raw-body 2.5.2
safe-buffer 5.2.1
safer-buffer 2.1.2
send 0.18.0
serve-static 1.15.0
set-function-length 1.2.2
setprototypeof 1.2.0
side-channel 1.0.6
socket.io 4.7.2
socket.io-adapter 2.5.2
socket.io-parser 4.2.4
statuses 2.0.1
toidentifier 1.0.1
type-is 1.6.18
undici-types 5.26.5
unpipe 1.0.0
utils-merge 1.0.1
vary 1.1.2
ws 8.11.0

required_toolboxes.txt pypi

ComputerVisionToolbox *
DataAcquisitionToolbox *
ImageProcessingToolbox *
InstrumentControlToolbox *
MATLAB *
OptimizationToolbox *
StatisticsandMachineLearningToolbox *

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