RU2494377C1 - Method of obtaining three-dimensional image of plankton sample - Google Patents

Abstract

FIELD: physics.

SUBSTANCE: X-ray micro-computed tomography of the sample is performed. The tomography process is performed over all objects contained in the sample, in which an X-ray contrast liquid is added to the fixing solution.

EFFECT: obtaining a three-dimensional image of a plankton sample, assembled using standard methods, with high refinement of objects.

Description

The present invention relates to the field of hydrobiological research and environmental monitoring, and can be used for automated processing of existing collections of fixed samples of zooplankton.

At present, a large number of zooplankton samples have been accumulated using standard methods (1). Biological objects in an aqueous sample contain a large amount of liquid in their body, similar in properties to water, which leads to their low radiopacity. After fixing the sample, the liquid inside the biological objects is replaced by a fixing solution and the objects in the sample remain non-contrast, which does not allow to obtain a high-quality three-dimensional image of the sample objects.

Known methods for laboratory processing of fixed samples of zooplankton containing many zooplankton objects, including obtaining images of samples in the visible part of the spectrum and further processing of this image, including the selection and identification of individual sample objects, quantitative and qualitative analysis of the sample (SIPPER - Shadowed Image Particle Profiling and Evaluation Recorder (2, 3),

Known methods have drawbacks in that, for automated processing, a plankton sample must be diluted in a large volume of water, followed by its placement in a thin flat layer or capillary, or a diluted sample must be passed through a cylindrical chamber of small diameter. As a result, there is a mechanical effect on the sample objects, which can lead to their partial destruction. With small dilution of the sample, there is a high probability of overlapping sample objects on top of each other, which subsequently significantly complicates or makes impossible their identification. Optical scanning or photographing of a limited sample volume is performed. Known methods have a limited size range of objects in which a qualitative analysis is carried out. This size range is different in different ways, for example: for SIPPER - 0.2-30 mm, for OPC - 0.25-2.5 mm, Flow CAM - 0.01-1 mm, ZooScan - 0.2-40 mm . Moreover, the size of biological objects can exceed the depth of field of the used lenses. Using known methods, two-dimensional images of the sample are formed with the biological objects contained in it, in which the information is in many cases insufficient for reliable identification of biological objects. In these cases, the success of identifying an object depends on the angle from which the objects are scanned or photographed and a two-dimensional image is obtained, and it is impossible to determine the desired angle in existing methods.

Known methods for obtaining a three-dimensional image of individual objects of zooplankton by tomography (4-6).

Known methods have the disadvantage that in order to obtain a three-dimensional image of an object, it must first be separated from the rest of the sample objects and then examined individually.

Closest to the proposed method for automated processing of fixed samples of zooplankton is a method for processing samples using x-ray microcomputer tomography (6). This method allows to obtain three-dimensional images of several biological objects together, but only when these objects are in an x-ray solid medium, in particular, this method is used to study biological objects in bottom sediments.

The proposed method allows the use of three-dimensional x-ray microcomputer tomography for a sample of zooplankton, including including non-contrast objects.

The aim of the present invention is to obtain a three-dimensional image of samples of zooplankton, collected by standard methods, with high detail objects. (The three-dimensional images of the samples obtained by the proposed method will subsequently allow a clear identification of the sample objects.) The goal is achieved by the fact that in the known method of X-ray microcomputer tomography, the entire set of objects contained in the sample is simultaneously subjected to the scanning process in which a radiopaque liquid is added to the fixing solution. In an embodiment of the method, the fixing solution in the sample is completely replaced with a radiopaque liquid.

Possibility of practical implementation

To implement the invention, it is necessary to add a radiopaque liquid to the sample to obtain the necessary degree of contrast of the objects (or replace the fixing solution with it) while preserving the biological objects in the sample. With the prepared sample, a standard X-ray microcomputer tomography procedure is performed. As a result of this procedure, a three-dimensional digital image of the set of objects contained in the sample is obtained, presented in the form of high-resolution three-dimensional images of the external contours of objects, where each object is presented in the form of a three-dimensional figure, which shows all the characteristic features of the surface of a particular object, necessary for subsequent automated analysis biological characteristics of the sample (reliable identification and biometry of objects, qualitative and quantitative analysis). The resulting 3D digital image allows the recognition of objects and measurement of geometric dimensions.

Computer analysis of a three-dimensional digital image of the sample and obtaining biological characteristics of the sample (reliable identification and biometry of objects, qualitative and quantitative analysis) significantly reduces the amount of routine work, improves the quality of information received about biological objects, and accelerates the processing of samples. Automated analysis does not require work by a highly qualified expert. An expert is only involved in pattern recognition that cannot be classified by the system.

The application of the method will allow to obtain a three-dimensional image of the zooplankton sample, which provides a quantitative and qualitative analysis of the sample in its digital image, without resorting to the primary biological sample. The digital image is not subject to degradation. It is possible to create backup copies of the sample, which eliminates their loss.

Information sources

1. Bogorov V.G. Standardization of marine planktonic studies // Proceedings of the Institute of Oceanology, 1957. V.24. S.200-214.

2. Samson S., Hopkins T., Remsen A., Langebrake L., Sutton T., Patten J. A system for high-resolution zooplankton imaging // IEEE Journal of Oceanic Engineering, 2001. Vol. 26. P.671-676.

3. Patent US 2004/0109586 A1

4. Patent US 7082182 B2.

5. Mazik K., Curtis N., Fagan MJ, Taft S., Elliott M. Accurate quantification of the influence of benthic macro- and meio-fauna on the geometric properties of estuarine muds by micro computer tomography // Journal of Experimental Marine Biology and Ecology, 2008. Vol. 354. P.192-201.

6. Dinley J., Hawkins L., Paterson G., Ball AD, Sinclair I., Sinnett-Jones P., Lanham S. Micro-computed X-ray tomography: a new non-destructive method of assessing sectional, fly- through and 3D imaging of a soft-bodied marine worm // Journal of Microscopy, 2010. Vol.238. P.123-133.

Claims (1)

A method of obtaining a three-dimensional digital image of an aqueous zooplankton sample with the objects contained in it, which consists in conducting an X-ray microcomputer tomography of the sample, characterized in that the entire set of objects contained in the sample is simultaneously subjected to the tomography process, in which a radiopaque liquid is added to the fixing solution.