Matrix-masking to balance nonuniform illumination in microscopy
Nordenfelt, Pontus LU
; Cooper, Jonathan M.
and Hochstetter, Axel
(2018)
In Optics Express
26(13).
p.17279-17288
- Abstract
With a perfectly uniform illumination, the amount and concentration of fluorophores in any (biological) sample can be read directly from fluorescence micrographs. However, non-uniform illumination in optical micrographs is a common, yet avoidable artefact, often caused by the setup of the microscope, or by inherent properties caused by the nature of the sample. In this paper, we demonstrate simple matrix-based methods using the common computing environments MATLAB and Python to correct nonuniform illumination, using either a background image or extracting illumination information directly from the sample image, together with subsequent image processing. We compare the processes, algorithms, and results obtained from both MATLAB... (More)
With a perfectly uniform illumination, the amount and concentration of fluorophores in any (biological) sample can be read directly from fluorescence micrographs. However, non-uniform illumination in optical micrographs is a common, yet avoidable artefact, often caused by the setup of the microscope, or by inherent properties caused by the nature of the sample. In this paper, we demonstrate simple matrix-based methods using the common computing environments MATLAB and Python to correct nonuniform illumination, using either a background image or extracting illumination information directly from the sample image, together with subsequent image processing. We compare the processes, algorithms, and results obtained from both MATLAB (commercially available) and Python (freeware). Additionally, we validate our method by evaluating commonly used alternative approaches, demonstrating that the best nonuniform illumination correction can be achieved when a separate background image is available.
(Less)
- author
- Nordenfelt, Pontus
LU
; Cooper, Jonathan M.
and Hochstetter, Axel
- organization
- publishing date
- 2018-06-25
- type
- Contribution to journal
- publication status
- published
- subject
- in
- Optics Express
- volume
- 26
- issue
- 13
- pages
- 10 pages
- publisher
- Optical Society of America
- external identifiers
-
- scopus:85049034044
- pmid:30119541
- ISSN
- 1094-4087
- DOI
- 10.1364/OE.26.017279
- language
- English
- LU publication?
- yes
- id
- ad013adc-8464-42db-b18a-149e04536eb5
- date added to LUP
- 2018-07-04 13:58:50
- date last changed
- 2024-03-18 11:36:00
@article{ad013adc-8464-42db-b18a-149e04536eb5,
abstract = {{<p>With a perfectly uniform illumination, the amount and concentration of fluorophores in any (biological) sample can be read directly from fluorescence micrographs. However, non-uniform illumination in optical micrographs is a common, yet avoidable artefact, often caused by the setup of the microscope, or by inherent properties caused by the nature of the sample. In this paper, we demonstrate simple matrix-based methods using the common computing environments MATLAB and Python to correct nonuniform illumination, using either a background image or extracting illumination information directly from the sample image, together with subsequent image processing. We compare the processes, algorithms, and results obtained from both MATLAB (commercially available) and Python (freeware). Additionally, we validate our method by evaluating commonly used alternative approaches, demonstrating that the best nonuniform illumination correction can be achieved when a separate background image is available.</p>}},
author = {{Nordenfelt, Pontus and Cooper, Jonathan M. and Hochstetter, Axel}},
issn = {{1094-4087}},
language = {{eng}},
month = {{06}},
number = {{13}},
pages = {{17279--17288}},
publisher = {{Optical Society of America}},
series = {{Optics Express}},
title = {{Matrix-masking to balance nonuniform illumination in microscopy}},
url = {{http://dx.doi.org/10.1364/OE.26.017279}},
doi = {{10.1364/OE.26.017279}},
volume = {{26}},
year = {{2018}},
}