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Cell Segmentation for Quantitative Analysis
Cell Segmentation and Tracking Data for High-Throughput Quantitative Analysis Contact: Dirk Padfield, GE Global Research, padfield@research.ge.com Paper references: Dirk Padfield, Jens Rittscher, and Badrinath Roysam, "Coupled min More »
6 years ago

Cell Segmentation and Tracking Data for High-Throughput Quantitative Analysis

Contact: Dirk Padfield, GE Global Research, padfield@research.ge.com

Paper references:

  1. Dirk Padfield, Jens Rittscher, and Badrinath Roysam, "Coupled minimum-cost flow cell tracking for high-throughput quantitative analysis", Medical Image Analysis 2011. http://dx.doi.org/10.1016/j.media.2010.07.006
  2. Dirk Padfield, Jens Rittscher, and Badrinath Roysam, "Coupled minimum-cost flow cell tracking", IPMI 2009. http://dx.doi.org/10.1007/978-3-642-02498-6_31
  3. Dirk Padfield, "Segmentation and tracking algorithms for monitoring cellular motion and function", RPI Ph.D. thesis 2009.

Abstract:

In the papers referenced above, five separate datasets were used to evaluate the accuracy of the segmentation and tracking algorithms introduced in those publications. The data were all generated at GE. This data is being made available to the public so that other researchers can run their algorithms on the datasets and compare results with the goal of enabling more direct comparison of various algorithms.

Data description:

The data were generated to test the accuracy of segmentation and tracking algorithms. The data consist of five time-lapse datasets with varying conditions and biological hypotheses and multiple wells as outlined in Table 2 of the article "Coupled minimum-cost flow cell tracking for high-throughput quantitative analysis." For all of the experiments, the wells were imaged on a GE IN Cell Analyzer 1000 with environmental control (37C, 5% CO2). The cell nuclei were stained with a nuclear DNA dye Hoechst, which is part of a family of fluorescent stains for labeling DNA in fluorescence microscopy. A number of the datasets were also stained with additional markers. Each dataset consists of images taken from different wells with many of the wells containing different doses of various treatments.

The following is a detailed description of these datasets:

![Dataset Descriptions](http://midas3.kitware.com/midas/thumbnailcreator/thumbnail/item?itemthumbnail=4 "Dataset Descriptions")

![Plate Layout](http://midas3.kitware.com/midas/thumbnailcreator/thumbnail/item?itemthumbnail=5 "Plate Layout")

L929

The movement of L929 mouse fibroblasts was monitored at 20X magnification (pixel spacing of 0.323 micrometers). This dataset includes both control wells and wells containing 10% horse serum, which is a source of growth factors and other agents promoting cell motility.

  • Goals: Measure motility of cells in wells with serum versus those without
  • Challenges: Defocus, stage shift, many cells
  • Control wells: columns 1-6
  • Treated wells: columns 7-12

L929a

The movement of L929 mouse fibroblasts was monitored at 20X magnification (pixel spacing of 0.323 micrometers). This dataset includes both control wells and wells containing 10% horse serum, which is a source of growth factors and other agents promoting cell motility.

  • Goals: Measure motility of cells in wells with serum versus those without
  • Challenges: Defocus, extreme stage shift, many cells
  • Control wells: columns 1-6
  • Treated wells: columns 7-12

HoechstStain3

The purpose of this experiment is the study of the effect of the cell-cycle inhibitor compound Roscovitine in HeLa cells by tracking the cells at 20X magnification (pixel spacing of 0.323 micrometers).

  • Goals: Measure cell cycle arrest induced by inhibitor compound
  • Challenges: Very low CNR
  • Control wells: column 2
  • Treated wells: column 3

HoechstStain2

In this experiment, the goal is to track a large number of cells at the low magnification of 10X (pixel spacing of 0.645 micrometers).

  • Goals: Measure cell motility
  • Challenges: Many cells, moving fast, low CNR
  • Control wells: column 4
  • Treated wells: None

ApplicationInst

The purpose of this experiment is to measure the cytoplasm to nucleus translocation of proteins, which is a key step in signal transduction from the cell cytoplasm to the nucleus in the control of gene expression. To accomplish this, the distribution of fluorescence throughout the cell reported by a STAT3-GFP fusion protein is measured. The magnification was 20X (pixel spacing of 0.323 micrometers).

  • Goals: Measure translocation of agonist from cytoplasm to nucleus
  • Challenges: Many cells, stage shift
  • Control wells: column 1
  • Treated wells: columns 2-12 with concentrations [0.19, 0.39, 0.78, 1.56, 3.12, 6.25, 12.5, 25, 50, 100, 300] ng/ml IL6
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