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Li D, Wang G, Werner R, Xie H, Guan JS, Hilgetag CC. Single Image-Based Vignetting Correction for Improving the Consistency of Neural Activity Analysis in 2-Photon Functional Microscopy. Front Neuroinform 2022; 15:674439. [PMID: 35069164 PMCID: PMC8766855 DOI: 10.3389/fninf.2021.674439] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Accepted: 12/01/2021] [Indexed: 12/04/2022] Open
Abstract
High-resolution functional 2-photon microscopy of neural activity is a cornerstone technique in current neuroscience, enabling, for instance, the image-based analysis of relations of the organization of local neuron populations and their temporal neural activity patterns. Interpreting local image intensity as a direct quantitative measure of neural activity presumes, however, a consistent within- and across-image relationship between the image intensity and neural activity, which may be subject to interference by illumination artifacts. In particular, the so-called vignetting artifact—the decrease of image intensity toward the edges of an image—is, at the moment, widely neglected in the context of functional microscopy analyses of neural activity, but potentially introduces a substantial center-periphery bias of derived functional measures. In the present report, we propose a straightforward protocol for single image-based vignetting correction. Using immediate-early gene-based 2-photon microscopic neural image data of the mouse brain, we show the necessity of correcting both image brightness and contrast to improve within- and across-image intensity consistency and demonstrate the plausibility of the resulting functional data.
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Affiliation(s)
- Dong Li
- Institute of Computational Neuroscience, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- *Correspondence: Dong Li,
| | - Guangyu Wang
- School of Life Sciences and Technology, ShanghaiTech University, Shanghai, China
| | - René Werner
- Institute of Computational Neuroscience, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Center for Biomedical Artificial Intelligence (bAIome), University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Hong Xie
- Institute of Photonic Chips, University of Shanghai for Science and Technology, Shanghai, China
- School of Health Science and Engineering, University of Shanghai for Science and Technology, Shanghai, China
| | - Ji-Song Guan
- School of Life Sciences and Technology, ShanghaiTech University, Shanghai, China
- Institute of Psychology, Chinese Academy of Sciences, Beijing, China
| | - Claus C. Hilgetag
- Institute of Computational Neuroscience, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Center for Biomedical Artificial Intelligence (bAIome), University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Department of Health Sciences, Boston University, Boston, MA, United States
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Jawale YK, Rapol U, Athale CA. Open Source 3D-printed focussing mechanism for cellphone-based cellular microscopy. J Microsc 2018; 273:105-114. [PMID: 30417401 DOI: 10.1111/jmi.12765] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2018] [Accepted: 10/16/2018] [Indexed: 11/28/2022]
Abstract
The need to improve access to microscopes in low-resource and educational settings coupled with the global proliferation of camera-enabled cellphones has recently led to an explosion in new developments in portable, low-cost microscopy. The availability of accurate ball lenses has resulted in many variants of van Leeuwenhoek-like microscopes. Combined with cellphones, they have the potential for use as portable microscopes in education and clinics. The need for reproducibility in such applications implies that control over focus is critical. Here, we describe a 3D-printed focussing mechanism based on a rack and pinion mechanism, coupled to a ball lens- based microscope. We quantify the time-stability of the focussing mechanism through an edge-based contrast measure used in autofocus cameras and apply it to 'thin smear' blood sample infected with Plasmodium as well as onion skin cells. We show that stability of the z-focus is in the micrometre range. This development could, we believe, serve to further enhance the utility of a low-cost and robust microscope and encourage further developments in field microscopes based on the Open Source principle. LAY DESCRIPTION: The wide spread of cellphones with cameras makes them an attractive platform for digital microscopy. Such microscopes could help improve microscope access in clinics and classrooms in the form of 'field microscopes', if they could be adapted for imaging cells. We integrate a 3D printed focussing mechanism made with recyclable plastic with ball-lens microscope of the Leeuwenhoek type. We demonstrate how the device can help stabilise to a focal plane for acquiring movies of a thin-smear of blood infected with Plasmodium and onion skin cells using a cellphone. The stability of focus is expectedly less precise as compared to research-grade microscopes, but is of the range of a few micrometers. We believe, the focussing device demonstrates it is possible to obtain reliable and reproducible images of typical samples used in clinics and classrooms. By making the design files of this device open-source we believe it could serve as a small step in improved, affordable and accurate 'field microscopes'.
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Affiliation(s)
- Y K Jawale
- Division of Biology, IISER Pune, Pune, India
| | - U Rapol
- Department of Physics, IISER Pune, Pune, India
| | - C A Athale
- Division of Biology, IISER Pune, Pune, India
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Colour Vignetting Correction for Microscopy Image Mosaics Used for Quantitative Analyses. BIOMED RESEARCH INTERNATIONAL 2018; 2018:7082154. [PMID: 29984245 PMCID: PMC6011154 DOI: 10.1155/2018/7082154] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/21/2018] [Revised: 04/30/2018] [Accepted: 05/10/2018] [Indexed: 01/01/2023]
Abstract
Image mosaicing permits achieving one high-resolution image, extending the visible area of the sample while keeping the same resolution. However, intensity inhomogeneity of the stitched images can alter measurements and the right perception of the original sample. The problem can be solved by flat-field correcting the images through the vignetting function. Vignetting correction has been widely addressed for grey-level images, but not for colour ones. In this work, a practical solution for the colour vignetting correction in microscopy, also facing the problem of saturated pixels, is described. In order to assess the quality of the proposed approach, five different tonal correction approaches were quantitatively compared using state-of-the-art metrics and seven pairs of partially overlapping images of seven different samples. The results obtained proved that the proposed approach allows obtaining high quality colour flat-field corrected images and seamless mosaics without employing any blending adjustment. In order to give the opportunity to easily obtain seamless mosaics ready for quantitative analysis, the described vignetting correction method has been implemented in an upgraded release of MicroMos (version 3.0), an open-source software specifically designed to automatically obtain mosaics of partially overlapped images.
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Bhadriraju K, Halter M, Amelot J, Bajcsy P, Chalfoun J, Vandecreme A, Mallon BS, Park KY, Sista S, Elliott JT, Plant AL. Large-scale time-lapse microscopy of Oct4 expression in human embryonic stem cell colonies. Stem Cell Res 2016; 17:122-9. [PMID: 27286574 PMCID: PMC5012928 DOI: 10.1016/j.scr.2016.05.012] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/17/2015] [Revised: 04/15/2016] [Accepted: 05/20/2016] [Indexed: 01/06/2023] Open
Abstract
Identification and quantification of the characteristics of stem cell preparations is critical for understanding stem cell biology and for the development and manufacturing of stem cell based therapies. We have developed image analysis and visualization software that allows effective use of time-lapse microscopy to provide spatial and dynamic information from large numbers of human embryonic stem cell colonies. To achieve statistically relevant sampling, we examined >680 colonies from 3 different preparations of cells over 5 days each, generating a total experimental dataset of 0.9 terabyte (TB). The 0.5 Giga-pixel images at each time point were represented by multi-resolution pyramids and visualized using the Deep Zoom Javascript library extended to support viewing Giga-pixel images over time and extracting data on individual colonies. We present a methodology that enables quantification of variations in nominally-identical preparations and between colonies, correlation of colony characteristics with Oct4 expression, and identification of rare events.
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Affiliation(s)
- Kiran Bhadriraju
- Department of Bioengineering, University of Maryland, College Park, MD 20742, USA
| | - Michael Halter
- Biosystems and Biomaterials Division, Materials Measurement Laboratory, National Institute of Standards and Technology, Gaithersburg, MD 20899, USA
| | - Julien Amelot
- Software Systems Division, Information Technology Laboratory, National Institute of Standards and Technology, Gaithersburg, MD 20899, USA
| | - Peter Bajcsy
- Software Systems Division, Information Technology Laboratory, National Institute of Standards and Technology, Gaithersburg, MD 20899, USA
| | - Joe Chalfoun
- Software Systems Division, Information Technology Laboratory, National Institute of Standards and Technology, Gaithersburg, MD 20899, USA
| | - Antoine Vandecreme
- Software Systems Division, Information Technology Laboratory, National Institute of Standards and Technology, Gaithersburg, MD 20899, USA
| | - Barbara S Mallon
- The NIH Stem Cell Unit, Division of Intramural Research, National Institute of Neurological Disorders and Stroke, NIH, U.S. Department of Health and Human Services, Bethesda, MD, USA
| | - Kye-Yoon Park
- The NIH Stem Cell Unit, Division of Intramural Research, National Institute of Neurological Disorders and Stroke, NIH, U.S. Department of Health and Human Services, Bethesda, MD, USA
| | - Subhash Sista
- Biosystems and Biomaterials Division, Materials Measurement Laboratory, National Institute of Standards and Technology, Gaithersburg, MD 20899, USA
| | - John T Elliott
- Biosystems and Biomaterials Division, Materials Measurement Laboratory, National Institute of Standards and Technology, Gaithersburg, MD 20899, USA
| | - Anne L Plant
- Biosystems and Biomaterials Division, Materials Measurement Laboratory, National Institute of Standards and Technology, Gaithersburg, MD 20899, USA
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Bajcsy P, Cardone A, Chalfoun J, Halter M, Juba D, Kociolek M, Majurski M, Peskin A, Simon C, Simon M, Vandecreme A, Brady M. Survey statistics of automated segmentations applied to optical imaging of mammalian cells. BMC Bioinformatics 2015; 16:330. [PMID: 26472075 PMCID: PMC4608288 DOI: 10.1186/s12859-015-0762-2] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2015] [Accepted: 10/07/2015] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND The goal of this survey paper is to overview cellular measurements using optical microscopy imaging followed by automated image segmentation. The cellular measurements of primary interest are taken from mammalian cells and their components. They are denoted as two- or three-dimensional (2D or 3D) image objects of biological interest. In our applications, such cellular measurements are important for understanding cell phenomena, such as cell counts, cell-scaffold interactions, cell colony growth rates, or cell pluripotency stability, as well as for establishing quality metrics for stem cell therapies. In this context, this survey paper is focused on automated segmentation as a software-based measurement leading to quantitative cellular measurements. METHODS We define the scope of this survey and a classification schema first. Next, all found and manually filteredpublications are classified according to the main categories: (1) objects of interests (or objects to be segmented), (2) imaging modalities, (3) digital data axes, (4) segmentation algorithms, (5) segmentation evaluations, (6) computational hardware platforms used for segmentation acceleration, and (7) object (cellular) measurements. Finally, all classified papers are converted programmatically into a set of hyperlinked web pages with occurrence and co-occurrence statistics of assigned categories. RESULTS The survey paper presents to a reader: (a) the state-of-the-art overview of published papers about automated segmentation applied to optical microscopy imaging of mammalian cells, (b) a classification of segmentation aspects in the context of cell optical imaging, (c) histogram and co-occurrence summary statistics about cellular measurements, segmentations, segmented objects, segmentation evaluations, and the use of computational platforms for accelerating segmentation execution, and (d) open research problems to pursue. CONCLUSIONS The novel contributions of this survey paper are: (1) a new type of classification of cellular measurements and automated segmentation, (2) statistics about the published literature, and (3) a web hyperlinked interface to classification statistics of the surveyed papers at https://isg.nist.gov/deepzoomweb/resources/survey/index.html.
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Affiliation(s)
- Peter Bajcsy
- Information Technology Laboratory, National Institute of Standards and Technology, Gaithersburg, USA.
| | - Antonio Cardone
- Information Technology Laboratory, National Institute of Standards and Technology, Gaithersburg, USA.
| | - Joe Chalfoun
- Information Technology Laboratory, National Institute of Standards and Technology, Gaithersburg, USA.
| | - Michael Halter
- Material Measurement Laboratory, National Institute of Standards and Technology, Gaithersburg, USA.
| | - Derek Juba
- Information Technology Laboratory, National Institute of Standards and Technology, Gaithersburg, USA.
| | | | - Michael Majurski
- Information Technology Laboratory, National Institute of Standards and Technology, Gaithersburg, USA.
| | - Adele Peskin
- Information Technology Laboratory, National Institute of Standards and Technology, Gaithersburg, USA.
| | - Carl Simon
- Material Measurement Laboratory, National Institute of Standards and Technology, Gaithersburg, USA.
| | - Mylene Simon
- Information Technology Laboratory, National Institute of Standards and Technology, Gaithersburg, USA.
| | - Antoine Vandecreme
- Information Technology Laboratory, National Institute of Standards and Technology, Gaithersburg, USA.
| | - Mary Brady
- Information Technology Laboratory, National Institute of Standards and Technology, Gaithersburg, USA.
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