DVDeconv: An Open-Source MATLAB Toolbox for Depth-Variant Asymmetric Deconvolution of Fluorescence Micrographs
To investigate the cellular structure, biomedical researchers often obtain three-dimensional images by combining two-dimensional images taken along the z axis. However, these images are blurry in all directions due to diffraction limitations. This blur becomes more severe when focusing further insid...
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| Format: | Article |
| Language: | English |
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MDPI AG
2021-02-01
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| Series: | Cells |
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| Online Access: | https://www.mdpi.com/2073-4409/10/2/397 |
| _version_ | 1797396514723594240 |
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| author | Boyoung Kim |
| author_facet | Boyoung Kim |
| author_sort | Boyoung Kim |
| collection | DOAJ |
| description | To investigate the cellular structure, biomedical researchers often obtain three-dimensional images by combining two-dimensional images taken along the z axis. However, these images are blurry in all directions due to diffraction limitations. This blur becomes more severe when focusing further inside the specimen as photons in deeper focus must traverse a longer distance within the specimen. This type of blur is called depth-variance. Moreover, due to lens imperfection, the blur has asymmetric shape. Most deconvolution solutions for removing blur assume depth-invariant or x-y symmetric blur, and presently, there is no open-source for depth-variant asymmetric deconvolution. In addition, existing datasets for deconvolution microscopy also assume invariant or x-y symmetric blur, which are insufficient to reflect actual imaging conditions. DVDeconv, that is a set of MATLAB functions with a user-friendly graphical interface, has been developed to address depth-variant asymmetric blur. DVDeconv includes dataset, depth-variant asymmetric point spread function generator, and deconvolution algorithms. Experimental results using DVDeconv reveal that depth-variant asymmetric deconvolution using DVDeconv removes blurs accurately. Furthermore, the dataset in DVDeconv constructed can be used to evaluate the performance of microscopy deconvolution to be developed in the future. |
| first_indexed | 2024-03-09T00:51:22Z |
| format | Article |
| id | doaj.art-4ac024497f4b4b30b97e6ff6551c7d11 |
| institution | Directory Open Access Journal |
| issn | 2073-4409 |
| language | English |
| last_indexed | 2024-03-09T00:51:22Z |
| publishDate | 2021-02-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Cells |
| spelling | doaj.art-4ac024497f4b4b30b97e6ff6551c7d112023-12-11T17:08:37ZengMDPI AGCells2073-44092021-02-0110239710.3390/cells10020397DVDeconv: An Open-Source MATLAB Toolbox for Depth-Variant Asymmetric Deconvolution of Fluorescence MicrographsBoyoung Kim0Robot R&D Group, Factory Automation Technology Team, Global Technology Center, Samsung Electronics, 129, Samsung-ro, Yeongtong, Suwon 443-742, Gyeonggi, KoreaTo investigate the cellular structure, biomedical researchers often obtain three-dimensional images by combining two-dimensional images taken along the z axis. However, these images are blurry in all directions due to diffraction limitations. This blur becomes more severe when focusing further inside the specimen as photons in deeper focus must traverse a longer distance within the specimen. This type of blur is called depth-variance. Moreover, due to lens imperfection, the blur has asymmetric shape. Most deconvolution solutions for removing blur assume depth-invariant or x-y symmetric blur, and presently, there is no open-source for depth-variant asymmetric deconvolution. In addition, existing datasets for deconvolution microscopy also assume invariant or x-y symmetric blur, which are insufficient to reflect actual imaging conditions. DVDeconv, that is a set of MATLAB functions with a user-friendly graphical interface, has been developed to address depth-variant asymmetric blur. DVDeconv includes dataset, depth-variant asymmetric point spread function generator, and deconvolution algorithms. Experimental results using DVDeconv reveal that depth-variant asymmetric deconvolution using DVDeconv removes blurs accurately. Furthermore, the dataset in DVDeconv constructed can be used to evaluate the performance of microscopy deconvolution to be developed in the future.https://www.mdpi.com/2073-4409/10/2/3973D microscopyfluorescence microscopydeconvolutionblind deconvolution |
| spellingShingle | Boyoung Kim DVDeconv: An Open-Source MATLAB Toolbox for Depth-Variant Asymmetric Deconvolution of Fluorescence Micrographs Cells 3D microscopy fluorescence microscopy deconvolution blind deconvolution |
| title | DVDeconv: An Open-Source MATLAB Toolbox for Depth-Variant Asymmetric Deconvolution of Fluorescence Micrographs |
| title_full | DVDeconv: An Open-Source MATLAB Toolbox for Depth-Variant Asymmetric Deconvolution of Fluorescence Micrographs |
| title_fullStr | DVDeconv: An Open-Source MATLAB Toolbox for Depth-Variant Asymmetric Deconvolution of Fluorescence Micrographs |
| title_full_unstemmed | DVDeconv: An Open-Source MATLAB Toolbox for Depth-Variant Asymmetric Deconvolution of Fluorescence Micrographs |
| title_short | DVDeconv: An Open-Source MATLAB Toolbox for Depth-Variant Asymmetric Deconvolution of Fluorescence Micrographs |
| title_sort | dvdeconv an open source matlab toolbox for depth variant asymmetric deconvolution of fluorescence micrographs |
| topic | 3D microscopy fluorescence microscopy deconvolution blind deconvolution |
| url | https://www.mdpi.com/2073-4409/10/2/397 |
| work_keys_str_mv | AT boyoungkim dvdeconvanopensourcematlabtoolboxfordepthvariantasymmetricdeconvolutionoffluorescencemicrographs |