CN102982521A - Artifact removal method for selective plane irradiation microscopy based on image superimposition - Google Patents
Artifact removal method for selective plane irradiation microscopy based on image superimposition Download PDFInfo
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- CN102982521A CN102982521A CN201210526194XA CN201210526194A CN102982521A CN 102982521 A CN102982521 A CN 102982521A CN 201210526194X A CN201210526194X A CN 201210526194XA CN 201210526194 A CN201210526194 A CN 201210526194A CN 102982521 A CN102982521 A CN 102982521A
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- 238000000034 method Methods 0.000 title claims abstract description 34
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- 238000003384 imaging method Methods 0.000 claims abstract description 59
- 241001270131 Agaricus moelleri Species 0.000 claims description 5
- 230000009467 reduction Effects 0.000 claims description 2
- 210000001072 colon Anatomy 0.000 description 11
- 230000015572 biosynthetic process Effects 0.000 description 9
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Images
Abstract
An artifact removal method for selective plane irradiation microscopy based on image superimposition comprises the steps of taking samples of images at the same position of focal planes vertically, conducting imaging on the same position of the samples, reducing noise of the images at the same position through weighted average, and obtaining whole images of the samples. The method can restrain the image noise, strip artifacts and scattering fuzz and improve imaging quality in the selective plane irradiation microscopy.
Description
Technical field
The present invention relates to a kind of selectivity plane irradiation micro-imaging SPIM technology, relate in particular to a kind of pseudo-shadow removal method of selectivity plane irradiation micro-imaging based on the doubling of the image.
Background technology
Selectivity plane irradiation microscopy is a kind of for the three-dimensional micro-imaging technique than the mcroorganism sample, and the mode that sample need to be cut and is fixed on the microslide from common microtechnic is different, and SPIM can observe the biological specimen of 1～20mm.In the SPIM imaging system, use laser instrument as light source, the CCD camera is as exploring block, and laser illumination direction and CCD camera are taken perpendicular direction.In the general low melting point agar with the sample insert molding, perhaps be encapsulated in the glass capillary, then agar or glass capillary are dipped in the glass flume that is contained with optical match liquid, the effect of optical match liquid is to prevent that light from producing serious refraction or reflection in sample surface.Laser instrument sends the parallel beam of even monochrome, and laser beam changes into the thin layer monochromatic collimated beam after by optical element, and the CCD camera focuses on the plane at thin layer light place by the front end microlens.Afterwards, move sample by agar or glass tube, make that an interested aspect is under the irradiation of thin layer light in the sample, the fluorescence excitation image of this aspect of CCD collected by camera, sample is carried out three-dimensional to be moved, such as translation, lifting etc., can collecting sample the fluorescence excitation image of inner diverse location, can realize at last the three-dimensional imaging of sample.
SPIM in imaging process because the difference of sample inner structure, can occur the high tissue that absorbs of light, these tissues can cause the strong attenuation of light, in that strip artifact and scattering to occur thereafter fuzzy, because light is absorbed the non-uniform phenomenon of rear appearance, serious noise can appear in the SPIM image simultaneously.
Summary of the invention
The purpose of this invention is to provide a kind of pseudo-shadow removal method of selectivity plane irradiation micro-imaging based on the doubling of the image.
For achieving the above object, a kind of pseudo-shadow removal method of selectivity plane irradiation micro-imaging based on the doubling of the image comprises:
For same position image on the focal plane, the vertical-lifting sample carries out repeatedly imaging to the sample same position;
With the multiple image of described same position, by the weighted mean noise reduction, obtain the general image of sample.
The present invention can realize that the inhibition that picture noise, strip artifact and scattering are fuzzy improves the quality of imaging in the selectivity plane irradiation micro-imaging.
Description of drawings
Fig. 1 is in the pseudo-shadow removal of the selectivity plane irradiation micro-imaging method of the embodiment of the invention based on the doubling of the image, about synoptic diagram and the corresponding result of formation method; Wherein, Fig. 1 a has shown common selectivity plane irradiation micro imaging method synoptic diagram, and wherein empty frame is imaging region; Fig. 1 b has shown that serious strip artifact appears in the local tomography image that collects under the method; The formation method synoptic diagram that the embodiment of the invention that shown Fig. 1 c adopts, empty frame are imaging region, by the scan mode of vertical-lifting sample the sample same position are carried out repeatedly overlapping imaging; Fig. 1 d has shown the local tomography result who obtains after image that the embodiment of the invention gathers is processed by weighted mean;
Fig. 2 is that imaging system is carried out the detailed process of image acquisition in the pseudo-shadow removal of the selectivity plane irradiation micro-imaging method of the embodiment of the invention based on the doubling of the image.Shown that detector focuses on the regional area on the sample, reached imaging region moving process synoptic diagram on sample when promoting sample;
Fig. 3 is that the embodiment of the invention is based on the data handling procedure in the pseudo-shadow removal of the selectivity plane irradiation micro-imaging method of the doubling of the image.Wherein, Fig. 3 a has shown that it is 30 weighting mask figure that every width of cloth topography is weighted weight limit that mean time uses, and Fig. 3 b has shown the overall schematic after all overlapping fritter amalgamations;
Fig. 4 is in the pseudo-shadow removal of the selectivity plane irradiation micro-imaging method of the embodiment of the invention based on the doubling of the image, carries out imaging for a certain section of mouse colon, adopts respectively traditional formation method and the inventive method to obtain result's comparison.The whole mouse colon tomograph of Fig. 4 a for using traditional formation method to draw; The whole mouse colon tomograph of Fig. 4 b for using the present invention to draw; Fig. 4 c, Fig. 4 d, Fig. 4 e and Fig. 4 f local mouse colon tomograph for using traditional formation method to draw; Fig. 4 g, Fig. 4 h, Fig. 4 i and Fig. 4 j local mouse colon tomograph for using the present invention to draw.The present invention can effectively improve picture quality as we can see from the figure.
Embodiment
For making the purpose, technical solutions and advantages of the present invention clearer, below in conjunction with specific embodiment, and with reference to accompanying drawing, the present invention is described in more detail.Although this paper can provide the demonstration of the parameter that comprises particular value, should be appreciated that parameter need not definitely to equal corresponding value, but can in acceptable error margin or design constraint, be similar to described value.
The present invention is a kind of pseudo-shadow removal method of selectivity plane irradiation micro-imaging based on the doubling of the image.It is fuzzy to the present invention is directed in the selectivity plane irradiation micro-imaging removal of images noise, strip artifact and scattering, scan mode by the vertical-lifting sample is carried out repeatedly overlapping imaging to the sample same position, and utilize image weighting average to suppress the various pseudo-shadow in the imaging, Effective Raise picture quality.As shown in Figure 1a, common selectivity plane irradiation micro-imaging can owing to the high object that absorbs in the light path causes imaging region strip artifact to occur, affect image quality in scanning; Shown in Fig. 1 b, strip artifact is obvious in the detector image-forming zone.Be the formation method synoptic diagram that the embodiment of the invention adopts such as Fig. 1 c, by the scan mode of vertical-lifting sample the sample same position carried out repeatedly overlapping imaging, namely each part can be by repeatedly imaging in the sample.The a large amount of superimposed images data that collect are weighted on average, draw the average image of sample.Fig. 1 d has shown the imaging effect figure of the inventive method, and the pseudo-shadow of visible imaging is greatly suppressed.The present invention carries out the high-quality imaging for the selectivity plane irradiation micro-imaging with situations such as noise, strip artifact and scattering are fuzzy specially.
Implementation of the present invention is divided into two key steps: Image Acquisition and data are processed, wherein, image acquisition step is by the vertical-lifting sample, the sample same position is carried out repeatedly overlapping imaging, can collect a large amount of superimposed images data of each part in the sample by this step, in these superimposed images data, only some jail-bar artifacts and scattering ambiguity occur, and most of image is all more clear.The data processing step image that these are overlapping is weighted on average according to position relationship, obtains the general image of sample, thereby suppresses noise, jail-bar artifacts and the problem such as fuzzy in some topography.The below utilizes the experiment of mouse colon to describe step of the present invention, adopts the mouse colon to carry out the selectivity plane irradiation micro-imaging of the doubling of the image in the experiment, and imaging system imaging region size is 3.8mm * 3.8mm; Image resolution ratio is 500 * 500; Each pixel size is 7.6 μ m; The distance of each vertically mobile 5 pixels of sample, i.e. 38 μ m; The total distance of sample vertical-lifting is 38mm, needs altogether mobile 1000 samples; Gather 1000 width of cloth images, the whole sample image size that obtains is 3.8mm * 38mm.If do not adopt the selectivity plane irradiation micro-imaging of the doubling of the image, need to gather 10 width of cloth images with the whole imaging of realization sample, but picture quality is relatively poor.Take the colon experiment as example, detailed step of the present invention is as follows:
Step S1: this step scans the image that gets access to a series of axial translations for selectivity plane irradiation micro-imaging, according to sample-size, calculates the distance that each step of sample promotes.By measuring, this sample is being of a size of 3.5mm * 38mm (size of different samples on a certain faultage image changes) on a certain faultage image, and the imaging region of imaging system is 3.8mm * 3.8mm (imaging region of different imaging systems is different).Image pixel size is to determine that by the actual imaging system relevant with hardware configuration, pixel size is 7.6 μ m in the present embodiment, and the each mobile step value of sample should be the integral multiple of image pixel size.Here we select the length of 5 pixels as the step value of each sample vertical-lifting, and then the step value of each sample lifting is 7.6 μ m*5=38 μ m; The number of times that sample need to promote is the ratio of sample height and step value, and namely 38mm/38 μ is m=1000 time; The multiplicity that each local location of sample is gathered is the ratio of imaging region height and step value, and the height of imaging region is 3.8mm, and the multiplicity that each local location is gathered is 3.8mm/38 μ m=100 time.General image is wide 3.8mm * high 38mm, and resolution is 500 * 5000, complete Covering samples, and wherein, the distance of vertical-lifting sample is less than the height in detector image-forming zone.As shown in Figure 2, detector focuses on first focal plane lastblock imaging region, and detector position is fixed.Regulate the focal plane, make it focus on above-mentioned selected fault surface.Determine the sample initial position, namely the sample upper end in the detector image-forming zone bottom.In the vertical-lifting sample, the beginning data acquisition, and recorded collection position, be convenient to the image subsequent treatment.When the leaving bottom detector and become the zone of sample, finish image acquisition, so far gather altogether 1000 images.This step can make that each regional area is gathered 100 times repeatedly in the sample, has greatly suppressed the noise effect of accidental appearance.
Step S2: the great amount of images that collects is weighted on average according to position relationship, obtains the general image of sample.Every width of cloth image is when being weighted, the weighting template of image adopts the flat-top pyramid weighting template figure shown in Fig. 3 a, the resolution of template figure is identical with image, be 500 * 500, the weighted value of weighting template figure zone line all is 30, the weighted value of 30 row or column at weighting template figure edge therefrom mind-set edge successively decreases 1 by row or by leu, utilize such weighting template figure, can weaken zone, image border shared proportion when weighted mean, thus the edge of topography in the level and smooth general image.Utilize flat-top pyramid weighting template, according to the position relationship weighted mean and piece together a width of cloth general image, general image is shown in Fig. 3 b with all images that collect in the present invention.
Selectivity plane irradiation micro-imaging to the described doubling of the image of the embodiment of the invention, Fig. 4 is that the embodiment of the invention is based on the selectivity plane irradiation micro imaging method of the doubling of the image, carry out imaging for a certain section of mouse colon, adopt respectively traditional formation method and the inventive method to obtain result's comparison.The whole mouse colon tomograph of Fig. 4 a for using traditional formation method to draw; The whole mouse colon tomograph of Fig. 4 b for using the present invention to draw; Fig. 4 c, Fig. 4 d, Fig. 4 e and Fig. 4 f local tomograph for using traditional formation method to draw; Fig. 4 g, Fig. 4 h, Fig. 4 i and Fig. 4 j local tomograph for using the present invention to draw.Can see that the present invention can effectively improve picture quality.
Above-described specific embodiment; purpose of the present invention, technical scheme and beneficial effect are further described; institute is understood that; the above only is specific embodiments of the invention; be not limited to the present invention; within the spirit and principles in the present invention all, any modification of making, be equal to replacement, improvement etc., all should be included within protection scope of the present invention.
Claims (9)
1. the pseudo-shadow removal method of micro-imaging is shone on the selectivity plane based on the doubling of the image, comprising:
For same position image on the focal plane, the vertical-lifting sample carries out repeatedly imaging to the sample same position;
With the multiple image of described same position, by the weighted mean noise reduction, obtain the general image of sample.
2. method according to claim 1 is characterized in that described vertical-lifting sample comprises:
The top of sample is placed the detector image-forming zone bottom, and the vertical-lifting sample is until the imaging region that shifts out bottom detector of sample.
3. method according to claim 2 is characterized in that the distance of vertical-lifting sample is less than the height in detector image-forming zone.
4. method according to claim 2 is characterized in that the ratio that the vertical mobile number of times of described sample is sample height and each mobile step value.
5. method according to claim 4 is characterized in that the each mobile step value of sample is the integral multiple of image pixel size.
6. method according to claim 1 is characterized in that the multiplicity that each local location of described sample is gathered is the ratio of imaging region height and step value.
7. method according to claim 1 is characterized in that adopting the flat-top pyramid model that multiple image is weighted on average.
8. method according to claim 7, the weight limit that it is characterized in that described flat-top pyramid model is 30.
9. method according to claim 7 is characterized in that the resolution of described flat-top pyramid model is identical with described image.
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| CN105989620A (en) * | 2015-03-16 | 2016-10-05 | 西门子公司 | Compensating for image artifacts in medical imaging |
| CN110853006A (en) * | 2019-11-05 | 2020-02-28 | 华南理工大学 | Method for evaluating quality of digital pathological image acquired by scanner |
| CN111563940A (en) * | 2020-07-15 | 2020-08-21 | 南京安科医疗科技有限公司 | Method for removing splicing artifacts in stepping axis scanning CT reconstruction and electronic medium |
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| CN101980284A (en) * | 2010-10-26 | 2011-02-23 | 北京理工大学 | Two-scale sparse representation-based color image noise reduction method |
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Cited By (5)
| Publication number | Priority date | Publication date | Assignee | Title |
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| CN105989620A (en) * | 2015-03-16 | 2016-10-05 | 西门子公司 | Compensating for image artifacts in medical imaging |
| CN105989620B (en) * | 2015-03-16 | 2019-03-22 | 西门子公司 | Compensate the image artifacts in medical imaging |
| CN110853006A (en) * | 2019-11-05 | 2020-02-28 | 华南理工大学 | Method for evaluating quality of digital pathological image acquired by scanner |
| CN110853006B (en) * | 2019-11-05 | 2020-06-23 | 华南理工大学 | Method for evaluating quality of digital pathological image acquired by scanner |
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Application publication date: 20130320 |