CN117593452A - Three-dimensional reconstruction method of radioworm micro-body fossil - Google Patents

Three-dimensional reconstruction method of radioworm micro-body fossil Download PDF

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CN117593452A
CN117593452A CN202311552970.8A CN202311552970A CN117593452A CN 117593452 A CN117593452 A CN 117593452A CN 202311552970 A CN202311552970 A CN 202311552970A CN 117593452 A CN117593452 A CN 117593452A
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sample
radiofossa
dimensional reconstruction
radioworm
micro
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陈倩
阳乐
李鑫
曹长群
方艳
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NANJING INST OF GEOLOGY AND PALEONTOLOGY CHINESE ACADEMY OF SCIENCES
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NANJING INST OF GEOLOGY AND PALEONTOLOGY CHINESE ACADEMY OF SCIENCES
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    • GPHYSICS
    • G06COMPUTING; CALCULATING OR COUNTING
    • G06TIMAGE DATA PROCESSING OR GENERATION, IN GENERAL
    • G06T17/00Three dimensional [3D] modelling, e.g. data description of 3D objects
    • GPHYSICS
    • G01MEASURING; TESTING
    • G01NINVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
    • G01N1/00Sampling; Preparing specimens for investigation
    • G01N1/28Preparing specimens for investigation including physical details of (bio-)chemical methods covered elsewhere, e.g. G01N33/50, C12Q
    • G01N1/36Embedding or analogous mounting of samples
    • GPHYSICS
    • G01MEASURING; TESTING
    • G01NINVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
    • G01N23/00Investigating or analysing materials by the use of wave or particle radiation, e.g. X-rays or neutrons, not covered by groups G01N3/00 – G01N17/00, G01N21/00 or G01N22/00
    • G01N23/22Investigating or analysing materials by the use of wave or particle radiation, e.g. X-rays or neutrons, not covered by groups G01N3/00 – G01N17/00, G01N21/00 or G01N22/00 by measuring secondary emission from the material
    • G01N23/2202Preparing specimens therefor
    • GPHYSICS
    • G01MEASURING; TESTING
    • G01NINVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
    • G01N23/00Investigating or analysing materials by the use of wave or particle radiation, e.g. X-rays or neutrons, not covered by groups G01N3/00 – G01N17/00, G01N21/00 or G01N22/00
    • G01N23/22Investigating or analysing materials by the use of wave or particle radiation, e.g. X-rays or neutrons, not covered by groups G01N3/00 – G01N17/00, G01N21/00 or G01N22/00 by measuring secondary emission from the material
    • G01N23/225Investigating or analysing materials by the use of wave or particle radiation, e.g. X-rays or neutrons, not covered by groups G01N3/00 – G01N17/00, G01N21/00 or G01N22/00 by measuring secondary emission from the material using electron or ion
    • G01N23/2251Investigating or analysing materials by the use of wave or particle radiation, e.g. X-rays or neutrons, not covered by groups G01N3/00 – G01N17/00, G01N21/00 or G01N22/00 by measuring secondary emission from the material using electron or ion using incident electron beams, e.g. scanning electron microscopy [SEM]

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Abstract

The invention discloses a three-dimensional reconstruction method of a radioworm micro-body fossil, belongs to the technical field of instrument testing, and aims to solve the problems that internal structure collapse is easy to occur in three-dimensional reconstruction of a focused ion beam scanning electron microscope, and reconstruction is disordered due to the fact that images comprise background information. The method comprises the steps of directionally embedding a radiofossa sample; determining an area to be analyzed of the radiofossa sample, and carrying out gold plating film treatment on the radiofossa sample; carrying out grooving pretreatment around the area to be analyzed, and carrying out finishing treatment on the section to be shot; adjusting the angle of the radiofossa fossil sample, and carrying out gold plating film treatment on the grooved surface formed after grooving; transferring the radiofossa sample obtained in the steps into a focused ion beam scanning electron microscope for imaging to obtain a series of section secondary electron images; and three-dimensional reconstruction is carried out on the obtained series of section secondary electron images by using Dramonfly software. The invention can be used for three-dimensional reconstruction of radiofossa.

Description

Three-dimensional reconstruction method of radioworm micro-body fossil
Technical Field
The invention belongs to the technical field of instrument testing, and particularly relates to a three-dimensional reconstruction method of radioworm micro-fossils, which can be widely applied to silicate radioworm fossils sample testing.
Background
The diameter of the individual radiofossa is about tens to hundreds of micrometers, the radiofossa is indistinguishable to naked eyes, the skeleton of the radiofossa is very exquisite, the structure is complex, the shape is different, microscopic imaging technology (for example, a scanning electron microscope) is generally used for observing the surface morphology and structure of the radiofossa, and the like, and the research on the morphology, ecology, and the like is carried out.
For samples with a size smaller than 1mm, there are generally three-dimensional structures of bones inside the sample obtained by three-dimensional reconstruction of a microscopic CT, three-dimensional reconstruction of a transmission electron microscope of a serial ultrathin section, three-dimensional reconstruction of a focused ion beam scanning electron microscope, and the like. The three-dimensional reconstruction of the focused ion beam scanning electron microscope is to continuously process a sample in three dimensions by utilizing Ga ion beams and acquire images of each section, however, as the inside of the radioactive insect sample is of a skeleton structure, the connection is often of point contact, and the holes are large and many, when continuous section information is acquired, the phenomenon of collapse of the internal structure can occur, and each image contains background information which does not belong to the current section after passing through a cavity, so that the later three-dimensional data reconstruction is disordered, and the effective characteristics of the sample can not be extracted.
Disclosure of Invention
In view of the above analysis, the present invention aims to provide a method for three-dimensional reconstruction of a radioworm micro-body fossil, which is used for solving the problems that in the prior art, the three-dimensional reconstruction of a focused ion beam scanning electron microscope is easy to generate internal structure collapse phenomenon, and the reconstruction is disordered due to the fact that an image comprises background information.
The aim of the invention is mainly realized by the following technical scheme:
the invention provides a three-dimensional reconstruction method of a radioworm micro-body fossil, which comprises the following steps:
step A: providing a radiofossa sample, and directionally embedding the radiofossa sample;
and (B) step (B): determining an area to be analyzed of the embedded and cured radiofossa sample, and carrying out gold plating film treatment on the embedded and cured radiofossa sample;
step C: carrying out grooving pretreatment around the area to be analyzed, and carrying out finishing treatment on the section to be shot;
step D: adjusting the angle of the radiofossa fossil sample, and carrying out gold plating film treatment on the grooved surface formed after grooving;
step E: transferring the radiofossa sample obtained in the step D into a focused ion beam scanning electron microscope for imaging to obtain a series of section secondary electron images;
step F: and three-dimensional reconstruction is carried out on the obtained series of section secondary electron images by using Dramonfly software.
Further, the embedding agent comprises 2 parts of bisphenol F epoxy resin and 1 to 1.2 parts of triethylene tetramine curing agent in parts by weight.
Further, in the step E, the imaging voltage is 1.5-5kV, and the imaging beam current is 100-300pA.
Further, the thickness of the gold film in the step B is 0.5-1 mu m; and D, the thickness of the gold film in the step is 20-100nm.
Further, in the step C, the grooving pretreatment comprises the following steps:
step C1: digging a trapezoid groove on the first side of the area to be analyzed;
step C2: square grooves are cut in the second and third sides adjacent to the first side.
Further, the Ga ion beam voltage of the trenching pretreatment was 30kV, and the beam current was 100nA or 65nA.
Further, in step C, the finishing process includes the steps of:
step C1': carrying out primary finishing on a section to be shot by adopting Ga ion beams with the voltage of 30kV and the beam current of 15 nA;
step C2': and (3) performing secondary trimming on the cross section subjected to primary trimming by adopting a Ga ion beam with the voltage of 30kV and the beam current of 1.5 nA.
Further, step D includes the steps of:
step D1: raising one side of the radiofossa sample to enable the first groove surface to face the direction of the metal spraying instrument target;
step D2: carrying out metal spraying treatment on the first groove surface, wherein the thickness of the metal film is 20-100nm;
step D3: raising the other side of the radiofossa sample so that the other groove surface faces the direction of the metal spraying instrument target;
step D4: and (3) carrying out metal spraying treatment on the other groove surface, wherein the thickness of the metal film is 20-100nm.
Further, in the step D1 and the step D3, the included angle between the base of the radiofossa sample and the sample stage of the metal spraying instrument is 10-30 degrees.
Further, step F includes the steps of:
step F1: introducing the secondary electron images of the series of sections into Dragonfly software, and performing preliminary cutting on the secondary electron images of the series of sections;
step F2: sequentially performing signal-to-noise ratio processing and correction, shadow processing and correction and alignment on the image after preliminary clipping;
step F3: performing threshold segmentation on the image processed in the step F2 based on the gray value to obtain a segmentation result;
step F4: and constructing a three-dimensional vector model from the segmentation result.
Compared with the prior art, the invention has at least the following beneficial effects:
the three-dimensional reconstruction method of the radioworm micro-fossils solves the problem of three-dimensional reconstruction of a specific area of the radioworm micro-fossils, and by carrying out directional embedding pretreatment, continuous cross-section sputtering and three-dimensional reconstruction on the radioworm micro-fossils sample with the dimension of 50-300 microns, a real three-dimensional internal structure restoration image without collapse of an area to be analyzed can be obtained, each cross-section secondary electron image only contains image information of a current sputtering cross section, invalid/interfering background information in the depth direction is shielded, real image information of each cross section of the radioworm fossils sample is automatically identified and extracted during three-dimensional reconstruction of data, so that double image phenomenon can be avoided, fossils can not be automatically identified based on gray scale, a large amount of manpower loss caused by manually removing the background image can be avoided, and the three-dimensional reconstruction efficiency of the internal skeleton of the radioworm micro-fossils is effectively improved.
Additional features and advantages of the invention will be set forth in the description which follows, and in part will be obvious from the description, or may be learned by practice of the invention. The objectives and other advantages of the invention may be realized and attained by the structure particularly pointed out in the written description and drawings.
Drawings
The drawings are only for the purpose of illustrating the invention and are not to be construed as limiting the invention, like reference numerals referring to like parts throughout the several views.
FIG. 1 is a schematic diagram of a grooved structure in a method for three-dimensionally reconstructing a radioworm micro-body fossil provided by the invention;
FIG. 2A is a three-dimensional perspective view of the interior of an unencapsulated radioworm original structure;
figure 2B is a continuous cross-sectional image of fossil of the first case without directional embedding;
FIG. 2C is a continuous cross-sectional image of fossil of a second case without directional embedding;
FIG. 3 is a photograph of a radiological insect after embedding with a resin according to an embodiment of the present invention;
FIG. 4 is a cross-sectional image of a artemia after embedding with a resin according to an embodiment of the present invention.
Reference numerals:
1-a trapezoid groove; 2-a region to be analyzed; 3-square grooves; 4-groove surface.
Detailed Description
The following detailed description of the preferred invention is provided in connection with the accompanying drawings, which form a part hereof, and together with the description serve to explain the principles of the invention.
The invention provides a three-dimensional reconstruction method of a radioworm micro-body fossil, which comprises the following steps:
step A: providing a radiofossa sample, and directionally embedding the radiofossa sample, wherein the embedding agent comprises 2 parts of bisphenol F epoxy resin and 1-1.2 parts of triethylene tetramine curing agent in parts by weight;
and (B) step (B): determining an area to be analyzed 2 of the embedded and solidified radiofossa fossil sample, and performing platinum film plating treatment (for example, platinum film) on the embedded and solidified radiofossa fossil sample to avoid damage caused by a Ga ion beam which is bombarded continuously;
step C: carrying out grooving pretreatment around the area 2 to be analyzed, and carrying out finishing treatment on the section to be shot;
step D: raising one side of the radiofossa sample by using plasticine, adjusting the angle of the radiofossa sample, and carrying out gold plating film treatment on the grooved surface 4 formed after grooving so as to improve the overall conductivity of the radiofossa sample;
step E: transferring the radiofossa sample obtained in the step D into a focused ion beam scanning electron microscope for imaging to obtain a series of section secondary electron images;
wherein the imaging voltage is 1.5-5kV, for example, 3kV, the imaging beam current is 100-300pA, for example, 200pA, so as to reduce charge accumulation on the radiofossa fossil sample, and the imaging process is set into a mode of cutting and scanning by an ion beam.
On the one hand, since Ga + The positive charge can neutralize negative charge accumulated in the process of scanning the cross section of the electron beam, further reduces the charge effect and improves the quality of the electron scanning picture of the cross section. On the other hand, by adjusting the imaging region size and the brightness contrast, and using a dynamic focusing function such that the upper and lower portions of the imaging region are always in focus, the single Zhang Jiemian scan image quality can be improved. In yet another aspect, continuous cross-section sputtering is achieved by providing a cross-section spacing.
Step F: and three-dimensional reconstruction is carried out on the obtained series of section secondary electron images by using Dramonfly software.
Compared with the prior art, the three-dimensional reconstruction method of the radioworm micro fossil solves the problem of three-dimensional reconstruction of a specific area of the radioworm micro fossil, and can obtain a real three-dimensional internal structure restoration image without collapse of an area to be analyzed 2 through directional embedding pretreatment, continuous cross-section sputtering and three-dimensional reconstruction of a radioworm micro fossil sample with the dimension of 50-300 microns, wherein each cross-section secondary electron image only contains image information of a current sputtering cross section, shielding background information invalid/interfering in the depth direction, and automatically identifying and extracting real image information of each cross section of the radioworm micro fossil sample during three-dimensional reconstruction of data, so that ghost phenomenon can be avoided, fossil cannot be automatically identified based on gray scale, a large amount of manpower loss caused by manually removing the background image can be avoided, and the three-dimensional reconstruction efficiency of internal bones of the radioworm micro fossil is effectively improved.
Specifically, on the one hand, the overall conductivity of the radiofossa sample can be improved and distortion of the electronic scanning image caused by the charging effect can be reduced by performing the gold plating film treatment on the grooved surface 4 formed after the grooving for the non-conductive characteristic of the radiofossa sample.
On the other hand, by directionally embedding the radiofossa fossil sample and adopting a specific embedding agent, each section secondary electron image only contains the image information of the current sputtering section, and the background information of invalidation and interference in the depth direction is shielded.
It should be noted that, the original structure of the embedded artemia is supported only by multiple points, the pores are more, see fig. 2A, if the directional embedding is not performed or an improper embedding agent is adopted, on one hand, the following situation may occur, when the ion beam cutting imaging is performed, the internal structure of the sample may suddenly collapse, the real fossil continuous section image cannot be obtained, see fig. 2B, the effective supporting point of the sample is displayed in the rectangular frame, the sample falls into the internal holes of the fossil, the important characteristics of the secondary electron image of the later series section are lost, and the structural characteristics not belonging to the area are further increased. On the other hand, the obtained series of images contains information not belonging to the current section, see fig. 2C, under the current section, the information displayed in the rectangular frame is background information, and should not appear in the current image, in which case, when the software is used for automatic recognition, the background information cannot be automatically subtracted. Image overlapping and deformation can occur during reconstruction, which greatly affects the three-dimensional reconstruction of the fossils structure.
In the step a, the directional embedding includes the following steps:
step 1: placing a radiofossa sample on a sample table, wherein the surface to be cut of the radiofossa sample faces upwards;
step 2: preparing an embedding agent, wherein the embedding agent comprises 2 parts by mass of bisphenol F epoxy resin and 1-1.2 parts by mass of triethylene tetramine curing agent;
step 3: under a microscope, sucking an embedding agent at the middle position by using a 0.1 mu L pipette, and dripping the embedding agent on the surface of the radiofossa sample so that the embedding agent is immersed in the surface of the radiofossa sample;
step 4: under a microscope, absorbing redundant embedding agent on the side surface of the radiofossa fossil sample by using low-dust paper (Kimtech) until the embedding agent uniformly covers the surface of the radiofossa fossil sample to obtain an embedded radiofossa fossil sample, so that the covering embedding agent is reduced as much as possible, the thickness of the embedding agent on the surface of the radiofossa fossil sample is reduced to be less than 50 mu m, and the consumption and sputtering time of a gallium ion source in the test process are reduced;
it should be noted that the height of the embedding agent is not lower than the highest position of the surface to be cut of the radiofossa fossil sample;
step 5: placing the embedded radiofossils sample into a closed cavity, opening a mechanical pump, and under the action of vacuum negative pressure, penetrating the embedding medium into the radiofossils sample to reduce pores and obtain a penetrated radiofossils sample;
step 6: and (3) placing the permeated radiofossils sample in an environment of 20-30 ℃ for 12-16 hours for full curing (the temperature rise peak value is less than 45 ℃ to avoid the deterioration of the permeated radiofossils sample), obtaining the radiofossils sample after embedding and curing, wherein the hardness of the embedding agent after curing is 80-90 HD, and the sputtering speed of the embedding agent by a gallium ion beam is similar to the sputtering speed of the radiofossils.
By adopting the directional embedding method, on one hand, the orientation of the radiofossils can be realized in the embedding process, the embedding depth of the radiofossils sample is controlled, the embedding agent can fully fill the inside of the radiofossils sample, the internal structure of the radiofossils sample is effectively supported, and the cured embedding agent has the sputtering rate close to that of the radiofossils sample, so that the next-step fine processing of gallium ion beams is more facilitated, the cross-section imaging of the appointed position of the radiofossils is realized, and time and resources can be saved while the brand-new internal information of the radiofossils sample is obtained. On the other hand, in the section secondary electron image obtained by the sample embedded by the embedding method, the contrast difference between fossil and embedding glue is large, analysis software can successfully identify and extract the image information of fossil, manual painting is not needed to distinguish information in pictures, labor cost investment can be effectively saved, and human interference factors are reduced.
Specifically, the step 1 includes the following steps:
step 11: adhering a double-sided conductive carbon paste (e.g., an aluminum-substrate type double-sided conductive carbon paste) to the sample stage;
step 12: placing the surface of the radiofossa specimen to be cut and sputtered upward (i.e., orienting the specimen);
step 13: the marten fossil sample is gently placed on the double-sided conductive carbon adhesive of the sample table by sticking a marten writing brush (with the diameter of 0.08 mm), and is finely adjusted to keep the original direction, see fig. 1.
In order to be able to obtain an embedding medium with a homogeneous texture and few bubbles, step 2 above comprises the following steps:
step 21: providing two parts of bisphenol F epoxy resin and one part of triethylene tetramine curing agent, and stirring and mixing the first part of bisphenol F epoxy resin and the one part of triethylene tetramine curing agent to obtain a first mixed solution; wherein, the mass ratio of the first bisphenol F epoxy resin to the triethylene tetramine curing agent is 1:1 to 1.2, and the stirring time is 5 to 10 minutes;
step 22: stirring and mixing the second part of bisphenol F epoxy resin and the first mixed solution until the texture is uniform, and obtaining an embedding agent; wherein, the mass ratio of the second bisphenol F epoxy resin to the triethylene tetramine curing agent is 1:1 to 1.2, the stirring time is 8 to 15 minutes, and the viscosity of the embedding agent is 800+/-50 mPa.S at the temperature of @25 ℃.
It should be noted that, the use of fine red mink hair can more easily locate a single designated fossil, is convenient to observe when turning over the fossil, and the soft hair does not harm fragile fossil samples.
In order to be able to reduce the occurrence of air bubbles, in step 21 above, a first part of bisphenol F epoxy resin is poured into a container (e.g., glass), and a triethylenetetramine curing agent is poured into the first part of bisphenol F epoxy resin along the inner wall of the container.
Similarly, in order to reduce the generation of bubbles, in the above step 22, a second part of bisphenol F epoxy resin is poured into the first mixed solution along the inner wall of the container.
In order to further reduce the generation of bubbles, in the step 21 and/or the step 22, stirring and mixing are performed by using a glass rod or a magnetic stirrer.
Illustratively, the above step 22 is followed by the steps of:
and defoaming the prepared embedding agent.
Specifically, the defoaming process includes the steps of:
step 23: placing an embedding agent into the closed cavity;
step 24: opening a mechanical pump to carry out vacuumizing, gradually overflowing bubbles under the action of vacuum negative pressure, closing the mechanical pump, and vacuumizing for 10-20 min according to the overflow condition of the bubbles;
step 25: sucking the embedding agent containing bubbles on the surface layer by using a plastic suction pipe and/or a pipetting gun;
step 26: steps 24 through 25 are repeated until the intermediate region of the embedding medium is free of macroscopic bubbles.
Specifically, the step B may include the steps of:
step B1: plating a layer of fine and uniform Au/Pt film on the surface of the embedded and solidified radiofossa sample;
step B2: moving the embedded and solidified radiofossa sample to a copolymerization focus of an electron beam and an ion beam;
step B3: and inserting a Pt gas injection device (GIS), and carrying out Pt plating treatment on the interested surface to be cut to protect the surface of the sample, wherein the thickness of the Au/Pt film is 0.5-1 mu m. Avoiding damage by the continuously bombarded Ga ion beam.
Specifically, in the step C, for the grooving pretreatment, see fig. 1, it includes the following steps:
step C1: digging a trapezoid groove on the first side of the area to be analyzed 2 for scanning observation of the electron beam;
step C2: square grooves 3 are cut in the second and third sides adjacent to the first side to prevent the ion beam from being anti-deposited when cutting the region 2 to be analyzed, and it should be noted that the occurrence of anti-deposition will affect the field of view of the scanned image.
Illustratively, the width of the trapezoid groove is larger than the width of the embedded and solidified radiofossa sample, and the length of the trapezoid groove is 1.5-2 times of the depth of the region 2 to be analyzed of the embedded and solidified radiofossa sample; the voltage of the Ga ion beam for the grooving pretreatment is 30kV, the beam current is 100nA or 65nA, and the embedding glue used in the step C can be used for carrying out the grooving pretreatment by adopting higher voltage and beam current and is rapid and efficient.
Accordingly, in the step C, for the finishing process, the steps include:
step C1': carrying out primary finishing on a section to be shot by adopting Ga ion beams with the voltage of 30kV and the beam current of 15 nA;
step C2': and (3) performing secondary trimming on the cross section subjected to primary trimming by adopting a Ga ion beam with the voltage of 30kV and the beam current of 1.5 nA.
In order to enable the effective gold plating treatment of the formed groove surface 4, the above-mentioned step D includes the steps of:
step D1: raising one side of the radiofossa sample to enable the first groove surface 4 to face the direction of the metal spraying instrument target material, wherein the included angle between the base of the radiofossa sample and the metal spraying instrument sample table is 10-30 degrees;
step D2: carrying out metal spraying treatment on the first groove surface 4, wherein the thickness of the metal film is 20-100nm;
step D3: raising the other side of the radiofossa sample to enable the other groove surface 4 to face the direction of the metal spraying instrument target material, wherein the included angle between the base of the radiofossa sample and the sample table of the metal spraying instrument is 10-30 degrees;
step D4: and (3) carrying out metal spraying treatment on the other groove surface 4, wherein the thickness of the metal film is 20-100nm.
In this way, the formed groove surface 4 is subjected to gold plating treatment, so that the situation that the periphery of a radiofossa fossil sample is plated with a conductive gold film as much as possible is ensured, the charge effect during shooting is reduced, the acquired image is clear and basically undistorted, and the quality of an electronic scanning picture of the cross section of the sample in the electron microscope can be obviously improved.
In order to enable three-dimensional reconstruction of the series of cross-section secondary electron images, the above step F comprises the steps of:
step F1: introducing a series of section secondary electron images (tiff format) into Dragonfly software, and performing preliminary cutting on the series of section secondary electron images;
step F2: sequentially performing signal-to-noise ratio processing and correction, shadow processing and correction and alignment on the image after preliminary clipping;
specifically, for signal-to-noise ratio processing and correction, a Median filter is used to perform non-local mean filtering on the current 2D initially cropped image, smooth denoising, and apply the same filtering process to all initially cropped images.
For shading and correction, there may be shadows at the edges of the picture due to some anti-deposition during the cutting process. The image after the signal-to-noise ratio processing and the correction processing of 2D was subjected to radial basis function filtering using a Radial Basis Function filter, the brightness of the image was adjusted with reference to the background gradation, and the same filtering processing was applied to the image after the signal-to-noise ratio processing and the correction processing.
For alignment, firstly, using the square sum function of differences in slice alignment, selecting the maximum conversion amplitude as Large, performing automatic alignment operation, if the correction effect is to be improved, repeatedly using the alignment function, and selecting the maximum conversion amplitude as Median or small for recalculation; then, all the section images are browsed and checked, and if a small number of images cannot be aligned by automatic adjustment, a manual correction function is selected for alignment piece by piece.
Step F3: and F2, carrying out threshold segmentation on the image processed in the step based on the gray value to obtain a segmentation result.
A threshold segmentation command is used, and the braking identification and segmentation conditions of the secondary electron scanning image are observed, so that the segmentation interface of the fossil region and the embedding glue region is clear and accurate by adjusting the range of the threshold; a new area is created, leaving only the fossils area as the area to be analyzed 2.
Step F4: and (5) structural output and three-dimensional model reconstruction.
And constructing a three-dimensional vector model for the segmentation result based on a mesh (polygonal mesh) technology, and outputting a mesh structure file, a raw format file or a video file.
Example 1
In this example, a 200 μm radiofossa was taken as an example, and three-dimensional reconstruction was performed based on secondary electron images. Specifically, the method for three-dimensional reconstruction of the radioworm micro-body fossil of the embodiment comprises the following steps:
adhering double-sided conductive carbon of an aluminum substrate type to a sample stage;
placing the surface to be cut and sputtered of a radiofossa fossil sample upwards;
sticking a radioworm fossil sample to a double-sided conductive carbon adhesive of a sample table by adopting a red mink writing brush with the diameter of 0.08mm, and fine-tuning to keep the original direction;
respectively weighing two parts of bisphenol F epoxy resin (10 g each part) and 10g of triethylene tetramine curing agent by using a glass cup, pouring 10g of the triethylene tetramine curing agent into the glass cup along the wall of the bisphenol F epoxy resin glass cup, and stirring at a low speed by using a glass rod for 5min to obtain a first mixed solution;
pouring 10g of bisphenol F epoxy resin into the first mixed solution along the wall of the glass cup, and stirring at a low speed for 8min until the texture is uniform to obtain an embedding agent;
placing the embedding agent into a closed cavity, opening a mechanical pump to vacuumize for 10min, gradually overflowing bubbles under vacuum negative pressure, closing the mechanical pump, sucking the embedding agent containing the bubbles on the surface layer by using a plastic suction pipe, and repeating the steps of vacuumizing and sucking the embedding agent until no bubbles are visible in the middle area of the embedding agent;
under a microscope, using a 0.1 mu L liquid transfer device to absorb liquid at the middle position of the embedding agent, and dripping the liquid on the surface of the radiofossa sample to enable the embedding agent to permeate the surface of the radiofossa sample;
under a microscope, absorbing redundant embedding agent on the side surface of the radiofossa sample by using low-dust paper (Kimtech) until the embedding agent uniformly covers the surface of the radiofossa sample, so as to obtain an embedded radiofossa sample;
placing the embedded radiofossils sample into a closed cavity, opening a mechanical pump, and penetrating the embedding medium into the radiofossils sample under the action of vacuum negative pressure to obtain a penetrated radiofossils sample;
placing the permeated radiofossa sample in an environment of 20 ℃ and keeping for 16 hours for full curing to obtain an embedded and cured radiofossa sample;
the embedding and curing of the radioworm image is shown in fig. 3, and it can be seen from fig. 3 that the resin pre-embedding of the radioworm can obtain a sample with the orientation, the embedding agent penetrating into the inner pores of the sample and the controlled thickness of the upper surface glue.
Referring to fig. 4, as can be seen from fig. 4, the method of the embodiment can effectively support the fossil area inside the sample, the section secondary electron image only contains the image information of the current sputtering section, the background information of invalidation/interference in the depth direction is shielded, fossil can be automatically identified based on gray scale, and therefore real and accurate three-dimensional reconstruction can be performed on the radioworm fossil sample.
And (3) performing platinum film plating treatment on the embedded and solidified radiofossa samples. And (5) placing the film-coated sample into a scanning electron microscope. The position of the surface to be cut of interest is moved to the copolymerization focus of the electron beam and the ion beam, a Pt GIS (gas injection device) is inserted, the Ga ion beam voltage and beam current are set to be 30kV,1.5nA, and the thickness of the finally deposited Pt protective layer is 0.5 mu m;
a trapezoid groove is dug in front of the area to be analyzed for scanning and observation by an electron beam. Two square grooves are dug on the side of the area to be analyzed to prevent the ion beam from being reversely deposited when cutting the area to be analyzed. If the reverse deposition occurs, the visual field of a scanned image is affected, the width of the trapezoid groove is larger than the section to be scanned of the sample, the length of the trapezoid groove is 1.5 times of the depth of the section to be scanned, and the voltage and the beam current of the Ga ion beam arranged in the groove are 30kV and 100nA;
carrying out finishing treatment on a section to be shot, firstly using a Ga ion beam of 30kV and 15nA, and then using a Ga ion beam of 30kV and 3 nA;
raising one side of the radiofossa sample to enable the first groove surface to face the direction of the metal spraying instrument target material, wherein the included angle between the base of the radiofossa sample and the metal spraying instrument sample table is 10 degrees; performing metal spraying film treatment on the first groove surface; the other side of the radiofossa sample is raised to enable the other groove surface to face the direction of the metal spraying instrument target, and the included angle between the base of the radiofossa sample and the sample table of the metal spraying instrument is 10 degrees.
The sample was then returned to the electron microscope for imaging using a lower secondary electron imaging voltage (3 kV) and beam current (200 pA). In the process of scanning the image, the method is set to a mode of cutting and scanning by an ion beam, the size and the brightness contrast of an imaging area are adjusted, and meanwhile, the upper part and the lower part of the imaging area can be always in focus by using a dynamic focusing function so as to improve the quality of the single Zhang Jiemian scanning image. By setting the section spacing, continuous section sputtering is realized, and a series of section secondary electron images are obtained;
importing the section secondary electron images (tiff format) of the sequences into Dragonfly software, and performing preliminary cutting on the pictures; non-local mean filtering is carried out on the current 2D picture by using a media filter, noise is removed smoothly, and the same filtering process is applied to all images; radial basis function filtering is performed on the current 2D picture by using a Radial Basis Function filter, brightness of the image is adjusted by referring to background gray scale, and the same filtering process is applied to all the images; using the square sum function of the difference in slice alignment, selecting the maximum conversion amplitude as Large, performing automatic alignment operation, if the correction effect is to be improved, repeatedly using the alignment function, and selecting the maximum conversion amplitude as Median or small for recalculation; browsing and checking all the section images, and if a small number of images cannot be aligned through automatic adjustment, selecting a manual correction function to align one by one; a threshold segmentation command is used, and the braking identification and segmentation conditions of the secondary electron scanning image are observed, so that the segmentation interface of the fossil region and the embedding glue region is clear and accurate by adjusting the range of the threshold; creating a new region, and reserving only the fossils region as a region of interest; and constructing a three-dimensional vector model on the basis of a mesh (polygonal mesh) technology on the segmentation result, and outputting a mesh structure file or a raw format file.
The obtained fossil continuous section image is shown in fig. 3, and as can be seen from fig. 3, the method of the embodiment can be used for truly and accurately reconstructing the three-dimensional radiofossa sample.
Example two
In this example, a 200 μm radiofossa was taken as an example, and three-dimensional reconstruction was performed based on secondary electron images. Specifically, the method for three-dimensional reconstruction of the radioworm micro-body fossil of the embodiment comprises the following steps:
adhering double-sided conductive carbon of an aluminum substrate type to a sample stage;
placing the surface to be cut and sputtered of a radiofossa fossil sample upwards;
sticking a radioworm fossil sample to a double-sided conductive carbon adhesive of a sample table by adopting a red mink writing brush with the diameter of 0.08mm, and fine-tuning to keep the original direction;
respectively weighing two parts of bisphenol F epoxy resin (10 g each) and 12g of triethylene tetramine curing agent by using a glass cup, pouring 12g of the triethylene tetramine curing agent into the glass cup along the wall of the bisphenol F epoxy resin glass cup, and stirring the glass cup at a low speed by using a magnetic stirrer for 8min to obtain a first mixed solution;
pouring 10g of bisphenol F epoxy resin into the first mixed solution along the wall of the glass cup, and stirring at a low speed for 12min until the texture is uniform to obtain an embedding agent;
placing the embedding agent into a closed cavity, opening a mechanical pump to vacuumize for 18min, gradually overflowing bubbles under vacuum negative pressure, closing the mechanical pump, sucking the embedding agent containing the bubbles on the surface layer by using a plastic suction pipe, and repeating the steps of vacuumizing and sucking the embedding agent until no bubbles are visible in the middle area of the embedding agent;
under a microscope, using a 0.1 mu L liquid transfer device to absorb liquid at the middle position of the embedding agent, and dripping the liquid on the surface of the radiofossa sample to enable the embedding agent to permeate the surface of the radiofossa sample;
under a microscope, absorbing redundant embedding agent on the side surface of the radiofossa sample by using low-dust paper (Kimtech) until the embedding agent uniformly covers the surface of the radiofossa sample, so as to obtain an embedded radiofossa sample;
placing the embedded radiofossils sample into a closed cavity, opening a mechanical pump, and penetrating the embedding medium into the radiofossils sample under the action of vacuum negative pressure to obtain a penetrated radiofossils sample;
placing the permeated radiofossa sample in an environment of 28 ℃ and keeping for 12 hours for full curing to obtain an embedded and cured radiofossa sample;
and (3) performing platinum film plating treatment on the embedded and solidified radiofossa samples. And (5) placing the film-coated sample into a scanning electron microscope. The position of the surface to be cut of interest is moved to the copolymerization focus of the electron beam and the ion beam, a Pt GIS (gas injection device) is inserted, the Ga ion beam voltage and beam current are set to be 30kV,1.5nA, and the thickness of the finally deposited Pt protective layer is 0.8 mu m;
a trapezoid groove is dug in front of the area to be analyzed for scanning and observation by an electron beam. Two square grooves are dug on the side of the area to be analyzed to prevent the ion beam from being reversely deposited when cutting the area to be analyzed. If the reverse deposition occurs, the visual field of a scanned image is affected, the width of the trapezoid groove is larger than the section to be scanned of the sample, the length of the trapezoid groove is 2 times of the depth of the section to be scanned, and the voltage and the beam current of the Ga ion beam arranged in the groove are 30kV and 65nA;
carrying out finishing treatment on a section to be shot, firstly using a Ga ion beam of 30kV and 15nA, and then using a Ga ion beam of 30kV and 1.5 nA;
raising one side of the radiofossa sample to enable the first groove surface to face the direction of the metal spraying instrument target material, wherein the included angle between the base of the radiofossa sample and the metal spraying instrument sample table is 25 degrees; performing metal spraying film treatment on the first groove surface; the other side of the radiofossa sample is raised to enable the other groove surface to face the direction of the target material of the metal spraying instrument, and the included angle between the base of the radiofossa sample and the sample table of the metal spraying instrument is 25 degrees. The sample was then returned to the electron microscope for imaging using a lower secondary electron imaging voltage (2 kV) and beam current (200 pA). In the process of scanning the image, the method is set to a mode of cutting and scanning by an ion beam, the size and the brightness contrast of an imaging area are adjusted, and meanwhile, the upper part and the lower part of the imaging area can be always in focus by using a dynamic focusing function so as to improve the quality of the single Zhang Jiemian scanning image. By setting the section spacing, continuous section sputtering is realized, and a series of section secondary electron images are obtained;
importing the section secondary electron images (tiff format) of the sequences into Dragonfly software, and performing preliminary cutting on the pictures; non-local mean filtering is carried out on the current 2D picture by using a media filter, noise is removed smoothly, and the same filtering process is applied to all images; radial basis function filtering is performed on the current 2D picture by using a Radial Basis Function filter, brightness of the image is adjusted by referring to background gray scale, and the same filtering process is applied to all the images; using the square sum function of the difference in slice alignment, selecting the maximum conversion amplitude as Large, performing automatic alignment operation, if the correction effect is to be improved, repeatedly using the alignment function, and selecting the maximum conversion amplitude as Median or small for recalculation; browsing and checking all the section images, and if a small number of images cannot be aligned through automatic adjustment, selecting a manual correction function to align one by one; a threshold segmentation command is used, and the braking identification and segmentation conditions of the secondary electron scanning image are observed, so that the segmentation interface of the fossil region and the embedding glue region is clear and accurate by adjusting the range of the threshold; creating a new region, and reserving only the fossils region as a region of interest; and constructing a three-dimensional vector model on the basis of a mesh (polygonal mesh) technology on the segmentation result, and outputting a mesh structure file or a raw format file.
The foregoing is only a preferred embodiment of the present invention, but the scope of the present invention is not limited thereto, and any changes or substitutions easily contemplated by those skilled in the art within the technical scope of the present invention should be included in the scope of the present invention.

Claims (10)

1. A method for three-dimensional reconstruction of a radioworm micro-body fossil, which is characterized by comprising the following steps:
step A: providing a radiofossa sample, and directionally embedding the radiofossa sample;
and (B) step (B): determining an area to be analyzed of the embedded and cured radiofossa sample, and carrying out gold plating film treatment on the embedded and cured radiofossa sample;
step C: carrying out grooving pretreatment around the area to be analyzed, and carrying out finishing treatment on the section to be shot;
step D: adjusting the angle of the radiofossa fossil sample, and carrying out gold plating film treatment on the grooved surface formed after grooving;
step E: transferring the radiofossa sample obtained in the step D into a focused ion beam scanning electron microscope for imaging to obtain a series of section secondary electron images;
step F: and three-dimensional reconstruction is carried out on the obtained series of section secondary electron images by using Dramonfly software.
2. The method for three-dimensional reconstruction of the radioworm micro-body fossil according to claim 1, wherein the composition of the embedding agent comprises 2 parts by mass of bisphenol F epoxy resin and 1-1.2 parts by mass of triethylene tetramine curing agent.
3. The method for three-dimensional reconstruction of radioworm micro-body fossil according to claim 1, wherein in the step E, the imaging voltage is 1.5-5kV, and the imaging beam current is 100-300pA.
4. The method for three-dimensional reconstruction of radioworm micro-body fossils according to claim 1, wherein the thickness of the gold film in the step B is 0.5-1 μm;
and D, the thickness of the gold film in the step is 20-100nm.
5. The method for three-dimensional reconstruction of radioworm micro-fossils according to claim 1, wherein in said step C, said trenching pretreatment comprises the steps of:
step C1: digging a trapezoid groove on the first side of the area to be analyzed;
step C2: square grooves are cut in the second and third sides adjacent to the first side.
6. The method for three-dimensional reconstruction of radioworm micro-foster according to claim 5, wherein the voltage of the Ga ion beam for the grooving pretreatment is 30kV, and the beam current is 100nA or 65nA.
7. The method of three-dimensional reconstruction of radioworm micro-fossils according to claim 1, wherein in step C, the finishing treatment comprises the steps of:
step C1': carrying out primary finishing on a section to be shot by adopting Ga ion beams with the voltage of 30kV and the beam current of 15 nA;
step C2': and (3) performing secondary trimming on the cross section subjected to primary trimming by adopting a Ga ion beam with the voltage of 30kV and the beam current of 1.5 nA.
8. The method of three-dimensional reconstruction of radioworm micro-fossils as defined in claim 1 wherein said step D comprises the steps of:
step D1: raising one side of the radiofossa sample to enable the first groove surface to face the direction of the metal spraying instrument target;
step D2: performing metal spraying film treatment on the first groove surface;
step D3: raising the other side of the radiofossa sample so that the other groove surface faces the direction of the metal spraying instrument target;
step D4: and (5) carrying out metal spraying treatment on the other groove surface.
9. The method of three-dimensional reconstruction of radiofossa micro-scale according to claim 8, wherein in the step D1 and the step D3, the angle between the base of the radiofossa sample and the specimen table of the metal spraying instrument is 10 ° to 30 °.
10. The method of three-dimensional reconstruction of radioworm micro-fossils according to claim 1, wherein said step F comprises the steps of:
step F1: introducing the secondary electron images of the series of sections into Dragonfly software, and performing preliminary cutting on the secondary electron images of the series of sections;
step F2: sequentially performing signal-to-noise ratio processing and correction, shadow processing and correction and alignment on the image after preliminary clipping;
step F3: performing threshold segmentation on the image processed in the step F2 based on the gray value to obtain a segmentation result;
step F4: and constructing a three-dimensional vector model from the segmentation result.
CN202311552970.8A 2023-11-21 2023-11-21 Three-dimensional reconstruction method of radioworm micro-body fossil Pending CN117593452A (en)

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