Histological quantification of maize stem sections from FASGA-stained images

Crop species are of increasing interest both for cattle feeding and for bioethanol production. The degradability of the plant material largely depends on the lignification of the tissues, but it also depends on histological features such as the cellular morphology or the relative amount of each tissue fraction. There is therefore a need for high-throughput phenotyping systems that quantify the histology of plant sections. We developed custom image processing and an analysis procedure for quantifying the histology of maize stem sections coloured with FASGA staining and digitalised with whole microscopy slide scanners. The procedure results in an automated segmentation of the input images into distinct tissue regions. The size and the fraction area of each tissue region can be quantified, as well as the average coloration within each region. The measured features can discriminate contrasted genotypes and identify changes in histology induced by environmental factors such as water deficit. The simplicity and the availability of the software will facilitate the elucidation of the relationships between the chemical composition of the tissues and changes in plant histology. The tool is expected to be useful for the study of large genetic populations, and to better understand the impact of environmental factors on plant histology.

• Publication year

  2017

• Venue

  Plant Methods

• Publication date

  2017-11-01

• Fields of study

  Biology, Medicine, Materials Science, Environmental Science

• Identifiers
  DOI 10.1186/s13007-017-0225-zPMID 29118822PMCID 5664815
• External record

  Open on Semantic Scholar

• Source metadata

  Semantic Scholar, PubMed

• Histological features including size, fraction area, and average coloration within each tissue region can discriminate contrasted genotypes and identify changes induced by environmental factors such as water deficit.

  Confidence 0.90

  All you need is Python (5d7gwfm5zu) extraction뀨 (7c402c1b98) review배휘동 (872fa5d2c9) reviewmexicorea (qjvnbu8xg3) review
• A custom image processing and analysis procedure enables automated segmentation of FASGA-stained maize stem section images into distinct tissue regions.

  Confidence 0.95

  All you need is Python (5d7gwfm5zu) extraction뀨 (7c402c1b98) review배휘동 (872fa5d2c9) reviewmexicorea (qjvnbu8xg3) review

• automated image segmentation

  method, computational technique

  A computational procedure that partitions digitalized microscopy images of stained sections into distinct tissue regions without manual intervention.

  Aliases: automated segmentation

  All you need is Python (5d7gwfm5zu) extraction뀨 (7c402c1b98) review배휘동 (872fa5d2c9) reviewmexicorea (qjvnbu8xg3) review
• fasga staining

  method, staining technique

  A histological staining method used to color maize stem sections, enabling visual differentiation of tissue types.

  Aliases: FASGA

  All you need is Python (5d7gwfm5zu) extraction뀨 (7c402c1b98) review배휘동 (872fa5d2c9) reviewmexicorea (qjvnbu8xg3) review
• genotype discrimination

  application, analytical task

  The ability to differentiate between genetic varieties of maize based on quantified histological features.

  All you need is Python (5d7gwfm5zu) extraction뀨 (7c402c1b98) review배휘동 (872fa5d2c9) reviewmexicorea (qjvnbu8xg3) review
• maize stem sections

  biological sample

  Cross-sectional slices of maize stems analyzed for cellular morphology and tissue composition.

  Aliases: maize stem section

  All you need is Python (5d7gwfm5zu) extraction뀨 (7c402c1b98) review배휘동 (872fa5d2c9) reviewmexicorea (qjvnbu8xg3) review
• tissue region quantification

  measurement, method

  Measurement of the size, fraction area, and average coloration within each segmented tissue region of maize stem sections.

  All you need is Python (5d7gwfm5zu) extraction뀨 (7c402c1b98) review배휘동 (872fa5d2c9) reviewmexicorea (qjvnbu8xg3) review
• water deficit

  environmental factor, experimental condition

  An environmental stress factor that induces measurable changes in plant histology.

  Aliases: drought, water stress

  All you need is Python (5d7gwfm5zu) extraction뀨 (7c402c1b98) review배휘동 (872fa5d2c9) reviewmexicorea (qjvnbu8xg3) review
• whole-slide microscopy scanning

  measurement technique, technology

  Digitalization of microscopy slides using whole-slide scanners to produce high-resolution images for computational analysis.

  Aliases: whole microscopy slide scanning

  All you need is Python (5d7gwfm5zu) extraction뀨 (7c402c1b98) review배휘동 (872fa5d2c9) reviewmexicorea (qjvnbu8xg3) review

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