Name: Single Cellome™ System SS2000
Brand: Yokogawa
SKU: ss2000

Single-cell and Subcellular Sampling System

The SS2000 is a dual microlens spinning disk confocal microscope for live-cell, high-content imaging which can sample adherent single cells and subcellular material while ensuring the preservation of spatial, morphological, and temporal information.

Single-Cell and Subcellular Sampling Process

SS2000 Single-Cell and Subcellular Sampling Overview

Automated, intuitive operation increases productivity and ease-of-use.
Image-based localization for accurate subcellular sampling.
Sampling maintains spatial and morphology information.
High resolution live cell imaging and image analysis using confocal microscopy.
Integrated incubator enables live cell experiments.
Flexible environmental control for maintaining integrity of collected samples.

Use Cases

	1) Direct sampling of intracellular components such as organelles or cytoplasm Intracellular components can be sampled at a single-cell level. This includes intracellular components that are difficult to sample by biochemical methods, such as organelles without lipid membranes.
	2) Sampling based on spatial information Positional information of sampling targets is maintained, which enables spatial biology experiments such as sampling and analyzing healthy cells adjacent to the cancer cells and those distant to the cancer cells.
	3) Sampling based on morphological information Morphological information of sampling targets is maintained, which allows analysis of cells of different morphologies and sampling based on morphological changes of each cell.
	4) Sampling specific cell regions Through high-resolution imaging and precise sampling, specific cell regions can be sampled. For example, different parts of a neuron, such as a cell body or axon, can be individually captured.
	5) Single-cell cloning of unique cells Single-cell cloning is possible from specific cells or cells with specific behavior under microscopic observation, such as transfected cells or virus-resistant cells. By combining high-resolution imaging and cell picking with morphological and spatial information, accurate and efficient cell cloning is possible.
	6) Collecting multiple samples into the same well Multiple samples can be collected in the same well for analyses that require larger sample amounts.

Subcellular sampling

Unlike existing cell isolation devices, the SS2000 can not only isolate a whole-cell but also sample subcellular content. It is possible to sample cytoplasm and regions containing target organelles selectively.

Mitochondria subcellular aspiration from HeLa cells

The images on the left showcase a HeLa cell with stained nuclei (blue), cytoplasm (green), and mitochondria (red). During this experiment, the mitochondria-rich region of the cytoplasm was sampled, as indicated by the red arrow.

Maintaining spatial and morphological information of target cells

Through the combination of the system’s high-resolution imaging with its precise sampling, target cells can be sampled without detaching other cells from the cell culture. In this manner, it is possible to maintain spatial and morphological information of target cells.

SS2000 Single-Cell Spatial Aspiration

The images on the left showcase normal MDCK cells and green fluorescent-labeled abnormal MDCK cells which were co-cultured at a 50:1 ratio. A normal cell which was adjacent to the abnormal cell and exhibiting fluorescent signals was sampled for downstream analysis, as indicated by the arrow.

Various downstream analysis options

Samples can be collected on PCR plates and on microplates, and multiple samples can be pooled in the same well. Samples can also be stored in the sampling tip without being ejected. The collector sector of the system has both a cooling function to suppress sample degradation and an incubator function to maintain an optimal environment for collected cells. These samples can be used in genomics, transcriptomics, proteomics, metabolomics, and single-cell cloning workflows.

Sample collection for genomics, transcriptomics, proteomics, metabolomics, and single-cell cloning

Live Cell Imaging with Confocal Microscopy

The SS2000 utilizes live-cell imaging products developed by Yokogawa. High-speed, high-resolution 3D imaging is possible using our unique confocal microscope technology. Samples can be taken from targeted cells under a confocal microscope in an incubator environment. Time-lapse imaging is also possible, allowing dynamic changes in the target cell to be captured. Since it is possible to record sampling videos as well as images before and after sampling, the SS2000 enables the combination of imaging data with downstream analysis data, such as mass spectrometry or sequencing, for a complete and holistic look at individual cells or their subcellular material.

SS2000 live-cell imaging and segmentation

Target cells and sampling positions can be automatically selected by image analysis. (Targets can be automatically selected as shape of cells, size of nuclei, density of organelles etc.)

Product Specifications

SS2000 Front

Automatic sampling functions	Tip diameter	3μm, 5μm, 8μm, 10μm
	Incubator loader environment	37℃, 5％CO₂, humidified
	Collection loader environment	37℃, 5％CO₂, humidified (for culture) / 4℃ (for cooling)
	Collection loader compatible vessels	96-well PCR plate (0.1mL, 0.2mL) Multiwell culture plate (96well)
	Postioning precision of sampling	XYZ axial designated resolution: 0.1μm
Imaging functions	Confocal scanning method	Microlens enhanced dual wide Nipkow disk confocal
	Incubator loader compatible vessels	When sampling cell: φ35mm dishes *1 Microplate (6well, 24well, 96well)
	Incubator loader compatible vessels	When observing cell: φ35mm dishes 1 Microplate (6well, 12well, 24well, 48well, 96well, 384well, 1536well) Slideglass 2
	Excitation laser wavelength	405, 488, 561, 640nm (Uniformizer installed)
	Emission filter	Filter size: φ25nm, Maximum slot number: 10 (Electric switching), Adjacent switching speed: 100msec
	Transmission illumination	Bright-field, LED source
	Objective lens	Dry lens:4x, 10x, 20x, 40x Long-working distance lens:20x, 40x Note that only the 40x dry lens can be used for cell sampling.
	Z focus	Electric Z motor, designated resolution:0.1μm
	Electric stage	XYZ axial designated resolution:0.1μm
	Autofocus	Laser autofocus
	Camera	sCMOS camera 2,000 x 2,000pixel Pixel size:6.5 x 6.5μm
Other	Special purpose workstation	Workstation for sampling, measurement, analysis, 24 inch display x2
	Measurement software	Measurement functions (2D, 3D, Time-lapse, Map imaging), Viewing measurement and sampling data, Reporting functions (Image data, Video data), Whole cell sampling, Intracellular component sampling
	Analysis software	Analysis functions (3D, Tile, Label-free, Texture analysis, Deep Learning, Gating), 3D viewer, Graphing functions, Reporting functions(Image data, Video data, EC50, IC50, Z'-factor)
	External dimensions, Weight	Main unit: W1,217 x D643 x H595 mm, 145kg Utility box: W275 x D432 x H298 mm, 18kg Gas mixer: W275 x D432 x H298 mm, 10kg Special purpose workstation: W172 x D471 x H414 mm, 14kg Display: W531 x D500 x H166 mm, 5.6kg
	Operating environment	Temperature: 15 to 30℃ Humidity: 30 to 70％RH　no condensation
	Power consumption	Main unit, Utility box and Gas mixer: 1,200VAmax Workstation: 950VAmax Display: 42VAmax x 2
	Data formats (Measurement software)	Captured images : 16bit TIFF (OME-TIFF, TIFF) Output image data : TIFF, PNG, JPEG Output video data : WMV, MPEG4
	Data formats (Analysis software)	Numeric data: CSV Output image data: TIFF, PNG, JPEG Output video data: WMV, MPEG4

*1 A sample holder is required, and with it, up to 3 samples can be installed.
*2 A sample holder is required, and with it, up to 4 samples can be installed.

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Frequently Asked Questions

What is single-cell analysis?

Unlike traditional bulk cell analysis, which analyzes samples of many cells and returns an average reading of all of them, single-cell analysis involves isolating individual cells and obtaining their unique data. For example, in a bulk proteomics experiment, a sample of various cells would be run through a mass spectrometer, which would output the average proteome of all those cells combined; on the other hand, a single-cell proteomics workflow might see an individual cell being run by the mass spectrometer, which would output that specific cell’s proteome.

Why is single-cell analysis important?

The importance of single-cell analysis lies in the fact that, even within the same cell line, cells are heterogeneous: they can showcase differences in behavior, responses to stimuli, and development, for example. Single-cell analysis can uncover this heterogeneity, unlike bulk experiments. Because of this, single-cell analysis can enable breakthroughs in fields like cell biology, personalized medicine, and oncology, to name a few.

With the Single CellomeTM System SS2000, can I sample from live cells?

Yes, the SS2000 is designed to sample from live cell cultures. Equipped with an incubator, the SS2000 can keep cultured cells alive for extended periods by controlling temperature, CO2 concentration, and humidity. This enables the user to image and sample from the same cell culture at many different time points, making it a powerful tool for temporal omics studies.

How is subcellular analysis possible?

As it is equipped with high-resolution confocal imaging technology, the SS2000 allows the user to identify the exact location of target intracellular material either through fluorescence or brightfield if fluorescence is not necessary. With this location information, the system punctures the cell using its microdiameter sampling tip and applies negative pressure to sample the target subcellular content.

How can I use the Single CellomeTM System SS2000 for single-cell cloning?

For single-cell cloning applications, the system is equipped with a gentle picking mode that uses capillary action and can pick certain cell types while maintaining their viability. These cells will then be placed in an incubated culture plate inside the SS2000 to promote single-cell cloning.

What are the main applications for the Single CellomeTM System SS2000?

The system can capture single-cell and subcellular samples for many downstream applications. For example, it can be a tool for single-cell or subcellular proteomics and metabolomics when positioned in a mass spectrometry workflow; alternatively, its samples can be discharged into sequencing kits for genomics and transcriptomics experiments.

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