CellPathfinder, High Content Analysis Software

CellPathfinder is designed for our HCA systems, CQ1 and the CellVoyager series. From beginners to experts, the analysis software lets you quantify subtle physiological changes and even label-free samples with various graph options.

Through the use of powerful machine learning algorithms, this software is capable of recognizing and analyzing patterns in images of unlabeled cells taken with bright-field microscopes. This software also has a 3D image analysis function for the observation of cells  that are being grown under 3D-conditions similar to a natural environment. This function makes it easy to quantify cell aggregate volume, surface area, and location.

Simple workflow from images to analysis and graphs


1. Display image data


2. Load and execute analysis protocol


・Easy-to-understand graphical icons
・Choose a preset template for your analysis

3. Gating

・ Specific populations can be extracted by gating the feature value data of recognized objects.

・The extracted populations can be analyzed further.

4. Make the graphs

・Various graph options to visualize the results
・The link between graph and images enables quick visual check of images by clicking data points

5. To examine further details…list the profiles of interesting cells

・Images and numerical data can be collected by clicking cells.

・Basic and Advance analysis modes are implemented.
・Beginners can perform quantitative analysis in Basic mode.
・Experts can flexibly customize the analysis in Advance mode.

◆3D analysis
・Analysis of Z-stack images in three-dimensional space.
・The volume and the location of objects in 3D space can be quantified.


◆Recognition of cytoskeleton by machine learning
・Software learns the features of the sample objects to analyze the images.


◆Label-free analysis
・Machine learning algorithm can recognize nuclei and cell bodies in unstained bright field images.

Corresponding system


  • Ultimate HCA system for high-quality imaging and high-throughput screening with water immersion objectives and multiple cameras
  • Built-in robot pipetter for kinetic assays
  • Bench top size confocal system
  • Simple operation and automated image acquisition of many sample
  • Live cell imaging

※Data acquired in CellVoyager CV1000 are not supported.
※CellPathfinder system contain the software and the workstation.

System configuration


Specifications of the workstation
Model: Dell Precision T5810XL
CPU: Intel® Xeon® E5-1620 v4
Memory:128 GB
HDD: System(C:) 4TB Storage, (D:) 4TB
OS: Windows® 10 Pro 64 bit Japanese/English
Display: 1920×1200, dual monitor


We have been developing a prototype of a genomic drug test support system using our CSU confocal scanner. This system administers chemical compounds that serve as potential drug candidates into living cells, which are the most basic components of all living organisms, records the changes in the amount and localization of target molecules inside cells with the CSU confocal scanner and a highly sensitive CCD camera, and processes and quantifies the captured high-resolution image data.

Yokogawa Technical Report
18.6 MB

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