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Data released on January 08, 2018

Supporting data for "Predicting plant biomass accumulation from image-derived parameters"

Chen, D; Shi, R; Pape, J, M; Neumann, K; Arend, D; Graner, A; Chen, M; Klukas, C (2018): Supporting data for "Predicting plant biomass accumulation from image-derived parameters" GigaScience Database. http://dx.doi.org/10.5524/100392 RIS BibTeX Text


Image-based high-throughput phenotyping technologies have been rapidly developed in plant science recently and they provide a great potential to gain more valuable information than traditionally destructive methods. Predicting plant biomass is regarded as a key purpose for plant breeders and ecologist. However, it is a great challenge to find a predictive biomass model across experiments.
In the present study, we constructed four predictive models to examine the quantitative relationship between image-based features and plant biomass accumulation. Our methodology has been applied to three consecutive barley (Hordeum vulgare) experiments with control and stress treatments. The results proved that plant biomass can be accurately predicted from image-based parameters using a random forest model. The high prediction accuracy based on this model will contribute to relieve the phenotyping bottleneck in biomass measurement in breeding applications. The prediction performance is still relatively high cross experiments under similar conditions. The relative contribution of individual features for predicting biomass was further quantified, revealing new insights into the phenotypic determinants of plant biomass outcome. Furthermore, the methods could also be used to determine the most important image-based features related to plant biomass accumulation, which would be promising for subsequent genetic mapping to uncover the genetic basis of biomass.
We have developed quantitative models to accurately predict plant biomass accumulation from image data. We anticipate that the analysis results will be useful to advance our views of the phenotypic determinants of plant biomass outcome, and the statistical methods can be broadly used for other plant species.

Contact Submitter

Read the peer-reviewed publication(s):

Chen, D., Shi, R., Pape, J.-M., Neumann, K., Arend, D., Graner, A., … Klukas, C. (2018). Predicting plant biomass accumulation from image-derived parameters. GigaScience, 7(2). doi:10.1093/gigascience/giy001

Additional information:

https://github.com/htpmod/HTPmod

Keywords:

Barley High-throughput phenotyping Phenomics Biomass Modeling 

Imaging, Software

http://gigadb.org/images/data/cropped/100392.jpg

Funding:

  • Funding body - Robert Bosch Stiftung
  • Award ID - 32.5.8003.0116.0
  • Awardee - C Klukas
  • Funding body - Federal Agency for Agriculture and Food
  • Award ID - 15/12-13 530-06.01-BiKo CHN
  • Awardee - C Klukas
  • Funding body - Bundesministerium für Bildung und Forschung
  • Award ID - 0315958A
  • Awardee - C Klukas
  • Funding body - Bundesministerium für Bildung und Forschung
  • Award ID - 031A053B
  • Awardee - C Klukas
  • Funding body - European Plant Phenotyping Network
  • Award ID - 284443
  • Awardee - C Klukas

Samples: Table Settings

Columns:

Common Name
Scienfic Name
Sample Attributes
Taxonomic ID
Genbank Name

Sample IDTaxonomic IDCommon NameGenbank NameScientific NameSample Attributes
1121KN0014513barley Hordeum vulgare Description:Barley cultivar BCC_1367_Apex grown fr...
Cultivar:BCC_1367_Apex
Perturbation:control
...
+
1121KN0024513barley Hordeum vulgare Description:Barley cultivar BCC_1367_Apex grown fr...
Cultivar:BCC_1367_Apex
Perturbation:control
...
+
1121KN0034513barley Hordeum vulgare Description:Barley cultivar BCC_1367_Apex grown fr...
Cultivar:BCC_1367_Apex
Perturbation:control
...
+
1121KN0044513barley Hordeum vulgare Description:Barley cultivar BCC_1367_Apex grown fr...
Cultivar:BCC_1367_Apex
Perturbation:control
...
+
1121KN0054513barley Hordeum vulgare Description:Barley cultivar BCC_1367_Apex grown fr...
Cultivar:BCC_1367_Apex
Perturbation:control
...
+
1121KN0064513barley Hordeum vulgare Description:Barley cultivar BCC_1367_Apex grown fr...
Cultivar:BCC_1367_Apex
Perturbation:control
...
+
1121KN0074513barley Hordeum vulgare Description:Barley cultivar BCC_1367_Apex grown fr...
Cultivar:BCC_1367_Apex
Perturbation:control
...
+
1121KN0084513barley Hordeum vulgare Description:Barley cultivar BCC_1367_Apex grown fr...
Cultivar:BCC_1367_Apex
Perturbation:control
...
+
1121KN0094513barley Hordeum vulgare Description:Barley cultivar BCC_1367_Apex grown fr...
Cultivar:BCC_1367_Apex
Perturbation:control
...
+
1121KN0104513barley Hordeum vulgare Description:Barley cultivar BCC_1367_Apex grown fr...
Cultivar:BCC_1367_Apex
Perturbation:stress
...
+
Displaying 1-10 of 936 Sample(s).

Files: (FTP site) Table Settings

Columns:

File Description
Sample ID
Data Type
File Format
Size
Release Date
Download Link
File Attributes

File NameSample IDData TypeFile FormatSizeRelease Date 
Tabular DataUNKNOWN128.22 KB2017-12-28
External linkUNKNOWN540.1 GB2017-12-28
Tabular DataUNKNOWN128.37 KB2017-12-28
External linkUNKNOWN555.8 GB2017-12-28
Tabular DataUNKNOWN126.62 KB2017-12-28
External linkUNKNOWN327.4 GB2017-12-28
1137KN001 +imageTAR86.29 MB2017-12-28
GitHub archivearchive651.09 KB2017-12-28
ReadmeTEXT3.11 KB2017-12-28
Displaying 1-9 of 9 File(s).

History:

+

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