SS2000 is a fully automated system that enables live-cell sampling of intracellular organelles — such as mitochondria and lysosomes — or even entire single cells, all while imaging cultured cells with a confocal microscope. There is no need to detach the cells from the culture dish beforehand, so spatial and morphological information remains intact. Several research publications have reported the use of SS2000 for sample collection followed by various omics analyses. Please refer to the “Publication Information” for details.
Live-Cell Imaging
Confocal microscopy enables high-speed, high-resolution 3D and time-lapse imaging of live cells.
Fully Automated, Reproducible Sampling
Automated extraction of single cells and organelles with spatial precision for reliable multi-omics analysis.
Uncover Disease Mechanisms at the Single-Cell Level
Downstream proteomic and genomic analysis reveals pathways involved in cancer and neurodegenerative diseases.
Details
Live-Cell Imaging with Confocal Microscopy
SS2000 is a system built on our proprietary live-cell imaging technology. With its unique confocal microscopy, it enables high-speed, high-resolution 3D imaging and supports time-lapse imaging to capture dynamic changes in target cells.

Target cells and sampling locations can be automatically selected through imaging analysis. (Targets are automatically selected based on cell shape, nucleus size, organelle density, etc.)
Subcellular Sampling
Sampling of target cells or intracellular components can be performed while observing them under an incubator environment. In addition, videos during sampling and images before and after sampling can be recorded, allowing users to correlate imaging data with analytical results of the collected samples.

Sampling of stress granules (FUS protein–GFP tag) in NIH/3T3 cells
Publication Information
Featuring studies that utilize our products.
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Title |
URL |
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|---|---|---|
| 1 | "Single-Cell Lipidomics by LC-MS Interlaboratory Study Reveals the Impact of X-ray Irradiation on a Pancreatic Cancer Cell Line and Its Bystanders" Kyle D. G. Saunders et al., Anal Chem. 2025 Jul 1;97(25):13532-13541. |
https://pubs.acs.org/doi/10.1021/acs.analchem.5c02010 |
|
2 |
"Mass spectrometric analysis of the amiodarone-induced alteration of phosphatidylcholines in living single cells" Aogu Furusho et al., J Pharm Biomed Anal. 2025 Jun 28:265:117045. |
https://www.sciencedirect.com/science/article/abs/pii/S0731708525003863 |
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3 |
"A subcellular sampling instrument allows spatial resolution of amyloid deposit-derived organelle-specific effects in microglia" Robert Subirana Slotos et al., Commun Biol. 2025 Jan 3;8(1):3. |
https://www.nature.com/articles/s42003-024-07405-w |
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4 |
"Single-Cell Untargeted Lipidomics Using Liquid Chromatography and Data-Dependent Acquisition after Live Cell Selection" Johanna von Gerichten et al., Anal Chem. 2024 May 7;96(18):6922-6929. |
https://pubs.acs.org/doi/10.1021/acs.analchem.3c05677 |
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5 |
"Advancing single cell technology: iSCseq drives living subcellular transcriptomic profiling in osteoimmune diversity" Hiroyuki Okada et al., bioRxiv. 2024 Mar |
https://www.biorxiv.org/content/10.1101/2022.09.05.506360v4 |
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6 |
"Analysis of Live Single Cells by Confocal Microscopy and High-Resolution Mass Spectrometry to Study Drug Uptake, Metabolism, and Drug-Induced Phospholipidosis" Liliana Pedro et al., Anal Chem. 2020 Dec 15;92(24):16005-16015. |
https://pubs.acs.org/doi/10.1021/acs.analchem.0c03534 |
Product Schematic and Post-analysis Image

Product Specifications

| 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) |
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| When observing cell : φ35mm dishes *1 Microplate (6well, 12well, 24well, 48well, 96well, 384well, 1536well) Slideglass *2 |
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| 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. |
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| 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 |
*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.
Yokogawa Life Science Official Social Media Accounts
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Please follow us.
| @Yokogawa_LS | |
| Yokogawa Life Science | |
| Yokogawa Life Science | |
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Yokogawa's Official Social Media Account List
Resources
In recent years, research on single cells has become increasingly popular, but with more sensitive analytical techniques, it has become possible to analyze specific intracellular components such as organelles at the single-cell level.
The SS2000 is an innovative system that can sample intracellular components at the single-cell level using a tip (glass capillary) with a diameter of several micrometers while imaging with a confocal microscope. In this application note, we introduce a case in which intracellular components were sampled by SS2000 and genetic analysis was performed by qPCR.
In recent years, single-cell studies have become increasingly popular as analytical techniques have become more sensitive and widespread.
The SS2000 is a revolutionary device that can sample intracellular components and single cells using glass capillary tips with a diameter of several micrometers while performing confocal microscope imaging. These application notes introduce examples of sampling for various cell types.
In recent years, single cell analysis has become increasingly popular due to the new development of advanced and high sensitivity analytical methods.
SS2000 is a revolutionary system that can sample subcellular components and a whole cell by using a glass capillary tip with an inner diameter of a few μm while imaging with a confocal microscope.
This application note provides an example of single cell RNA sequencing scRNA seq) from cells sampled by SS2000, and the data is comparable to conventional methods.
In recent years, research on single cells has become increasingly popular. With more sensitive analytical techniques, it has become possible to analyze specific intracellular components such as organelles, even at the single-cell level.
The SS2000 is an innovative system that can sample subcellular intracellular components using a glass capillary having a tip diameter of only a few micrometers while imaging with a confocal microscope.
In this application note, we introduce a case where after drug treatment, intracellular components were sampled by the SS2000 and analyzed by single-cell mass spectrometry.
The SS2000 is a revolutionary system that allows both confocal imaging and sampling of targeted intracellular components or single cells using a glass tip with an inner diameter of a few micrometers. The SS2000 includes an incubator as well as highcontent imaging functions, such as long time-lapse observation, machine learning, and label-free analysis.
The SU10 is an innovative device that delivers target substances directly into cells or into nuclei with a nanopipette that has a tip outer diameter as small as a few tens nm.
This application note shows a case study of sampling and analysis with the SS2000 from cells delivered intracellularly with the SU10.
In recent years, single-cell studies have become increasingly popular, leading to the development of instruments capable of spatial omics - the integration of samples' 3D locations and their omics data. The SS2000 is a revolutionary device that can collect intracellular components at the single-cell level and image the samples using a confocal microscope. In this application note we introduce the research performed by Dr. Okada of The University of Tokyo, who established an intra single living cell sequencing (iSC-seq) method which uses SS2000 to sample intracellular components from osteoclasts (a type of multinucleated giant cell) and analyzes them through next-generation sequencing.
In recent years, research on single cells has been actively conducted.However, with more sensitive analytical techniques, it is now possible to analyze specific intracellular components at the single-cell level.
Downloads
Brochures
- Single Cellome System SS2000 Catalog (11.1 MB)
Videos
YOKOGAWA will contribute to technology evolution particularly in measurement and analytical tools to help build a world where researchers will increasingly focus on insightful interpretation of data, and advancing Life Science to benefit humanity.
The Yokogawa business vision states that the company endeavors to achieve Net-zero emissions, ensure the Well-being of all, and make a transition to a Circular Economy by 2050.
Explore single-cell lipidomics and cell diversity with Yokogawa’s SS2000 in this on-demand webinar. Featuring Kyle Saunders from the University of Surrey’s SEISMIC facility, learn mass spectrometry insights and more—watch now!
News
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News Brief Apr 26, 2024 Yokogawa Helps to Revolutionize the Field of Single-Cell Lipidomics
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Press Release | Solutions & Products Dec 1, 2021 Yokogawa Develops Single Cellome System SS2000 for Subcellular Sampling
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