Adaptive image‐processing technique and effective visualization of confocal microscopy images

Sun, Yinlong; Rajwa, Bartek; Robinson, J. Paul

doi:10.1002/jemt.20064

Cited by 27 publications

(21 citation statements)

References 34 publications

(34 reference statements)

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“…Second, the method must be robust to various acquisition artifacts that are specific to confocal microscopy. [25][26][27][28] Last, the large amount of data that is involved imposes a subtle balance between memory and time constraints.…”

Section: Introductionmentioning

confidence: 99%

Four-dimensional cardiac imaging in living embryos via postacquisition synchronization of nongated slice sequences

et al. 2005

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Abstract. Being able to acquire, visualize, and analyze 3D time series ͑4D data͒ from living embryos makes it possible to understand complex dynamic movements at early stages of embryonic development. Despite recent technological breakthroughs in 2D dynamic imaging, confocal microscopes remain quite slow at capturing optical sections at successive depths. However, when the studied motion is periodicsuch as for a beating heart-a way to circumvent this problem is to acquire, successively, sets of 2D + time slice sequences at increasing depths over at least one time period and later rearrange them to recover a 3D + time sequence. In other imaging modalities at macroscopic scales, external gating signals, e.g., an electro-cardiogram, have been used to achieve proper synchronization. Since gating signals are either unavailable or cumbersome to acquire in microscopic organisms, we have developed a procedure to reconstruct volumes based solely on the information contained in the image sequences. The central part of the algorithm is a least-squares minimization of an objective criterion that depends on the similarity between the data from neighboring depths. Owing to a wavelet-based multiresolution approach, our method is robust to common confocal microscopy artifacts. We validate the procedure on both simulated data and in vivo measurements from living zebrafish embryos.

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Section: Introductionmentioning

confidence: 99%

Four-dimensional cardiac imaging in living embryos via postacquisition synchronization of nongated slice sequences

et al. 2005

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“…However, the image data sets acquired by LSCM show several characteristics requiring special processing techniques to make the method applicable [1,3,4]:…”

Section: Principles Of Laser Scanning Confocal Microscopymentioning

confidence: 99%

“…LSCM is relatively new in obtaining tomographic structures in the microscopic scale [1][2][3][4][5][6][7], probably due to the relative ease to acquire high quality images from specimens and the growing number of applications in cell biology relying on imaging fixed and living cells or tissues. However, how to process confocal data sets still remains a puzzle.…”

Section: Introductionmentioning

confidence: 99%

Image Processing and Interactive Visualization of Confocal Microscopy Images

Tang

Wang

2008

Journal of Algorithms & Computational Technology

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The essence and methodology is proposed for image processing and interactive visualization of confocal microscopy images. Firstly, an intensity compensation algorithm is applied to reduce noises resulted from light absorption and scattering by objects and particles in the volume through which light passed. Secondly, a deconvolution algorithm based on Maximum A Posteriori is applied to improve the image stacks' quality. Lastly, the raycasting algorithm is used to reconstruct the fine details in the volume. Furthermore, interactive control panel is integrated to provide users an intuitive interface to view the cells and its structures through translation, rotation and zoom in/out operations. Experimental results demonstrate that the speed and versatility of the program allows for convenient, fast, interactive examination of unknown cell structures even on commodity PC without any other special hardware. The program is also able to visualize dynamically changing temporary structures conveniently in addition to static images.

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“…Many of them use especially the exponential decay law for modeling the light attenuation with depth because of scattering, absorption, and photobleaching (Ghauharali and Brakenhoff, 1998;Ghauharali and Brakenhoff, 2000;Kervrann et al, 2004;Markham and Conchello, 2001;Rodenacker et al, 2001;Sun et al, 2004). A method based on the study of a stack of 2D histograms formed from each consecutive pair of optical sections was applied to calculate the attenuation factor (Liljeborg et al, 1995).…”

Section: Introductionmentioning

confidence: 99%

Methods for compensation of the light attenuation with depth of images captured by a confocal microscope

Čapek

Janáček

Kubínová

2006

Microsc. Res. Tech.

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A confocal laser scanning microscope (CLSM) enables us to capture images from a biological specimen in different depths and obtain a series of precisely registered fluorescent images. However, images captured from deep layers of the specimen may be darker than images from the topmost layers because of light loss distortions. This effect causes difficulties in subsequent analysis of biological objects. We propose a solution using two approaches: either an online method working already during image acquisition or an offline method assisting as a postprocessing step. In the online method, the gain value of a photomultiplier tube of a CLSM is controlled according to the difference of mean image intensities between the reference and currently acquired image. The offline method consists of two stages. In the first stage, a standard histogram maintaining relative frequencies of gray levels and improving brightness and contrast is created from all images in the series. In the second stage, individual image histograms are warped according to this standard histogram. The methods were tested on real confocal image data captured from human placenta and rat skeletal muscle specimens. It was shown that both approaches diminish the light attenuation in images captured from deep layers of the specimen.

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Adaptive image‐processing technique and effective visualization of confocal microscopy images

Cited by 27 publications

References 34 publications

Four-dimensional cardiac imaging in living embryos via postacquisition synchronization of nongated slice sequences

Four-dimensional cardiac imaging in living embryos via postacquisition synchronization of nongated slice sequences

Image Processing and Interactive Visualization of Confocal Microscopy Images

Methods for compensation of the light attenuation with depth of images captured by a confocal microscope

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