An improved method for the segmentation of roots from X-ray computed tomography 3D images : (Record no. 64128)
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| 000 -LEADER | |
|---|---|
| fixed length control field | nab a22 7a 4500 |
| 001 - CONTROL NUMBER | |
| control field | 64128 |
| 003 - CONTROL NUMBER IDENTIFIER | |
| control field | MX-TxCIM |
| 005 - DATE AND TIME OF LATEST TRANSACTION | |
| control field | 20210902154526.0 |
| 008 - FIXED-LENGTH DATA ELEMENTS--GENERAL INFORMATION | |
| fixed length control field | 200320s2021 xxk|||p|op||| 00| 0 eng d |
| 022 ## - INTERNATIONAL STANDARD SERIAL NUMBER | |
| International Standard Serial Number | 1746-4811 |
| 024 8# - OTHER STANDARD IDENTIFIER | |
| Standard number or code | https://doi.org/10.1186/s13007-021-00735-4 |
| 040 ## - CATALOGING SOURCE | |
| Original cataloging agency | MX-TxCIM |
| 041 ## - LANGUAGE CODE | |
| Language code of text/sound track or separate title | eng |
| 100 1# - MAIN ENTRY--PERSONAL NAME | |
| 9 (RLIN) | 22448 |
| Personal name | Phalempin, M. |
| 245 13 - TITLE STATEMENT | |
| Title | An improved method for the segmentation of roots from X-ray computed tomography 3D images : |
| Remainder of title | rootine v.2 |
| 260 ## - PUBLICATION, DISTRIBUTION, ETC. (IMPRINT) | |
| Place of publication, distribution, etc. | London (United Kingdom) : |
| Name of publisher, distributor, etc. | BioMed Central, |
| Date of publication, distribution, etc. | 2021. |
| 500 ## - GENERAL NOTE | |
| General note | Peer review |
| 500 ## - GENERAL NOTE | |
| General note | Open Access |
| 520 ## - SUMMARY, ETC. | |
| Summary, etc. | Background: X-ray computed tomography is acknowledged as a powerful tool for the study of root system architecture of plants growing in soil. In this paper, we improved the original root segmentation algorithm “Rootine” and present its succeeding version “Rootine v.2”. In addition to gray value information, Rootine algorithms are based on shape detection of cylindrical roots. Both algorithms are macros for the ImageJ software and are made freely available to the public. New features in Rootine v.2 are (i) a pot wall detection and removal step to avoid segmentation artefacts for roots growing along the pot wall, (ii) a calculation of the root average gray value based on a histogram analysis, (iii) an automatic calculation of thresholds for hysteresis thresholding of the tubeness image to reduce the number of parameters and (iv) a false negatives recovery based on shape criteria to increase root recovery. We compare the segmentation results of Rootine v.1 and Rootine v.2 with the results of root washing and subsequent analysis with WinRhizo. We use a benchmark dataset of maize roots (Zea mays L. cv. B73) grown in repacked soil for two scenarios with differing soil heterogeneity and image quality. Results: We demonstrate that Rootine v.2 outperforms its preceding version in terms of root recovery and enables to match better the root diameter distribution data obtained with root washing. Despite a longer processing time, Rootine v.2 comprises less user-defined parameters and shows an overall greater usability. Conclusion: The proposed method facilitates higher root detection accuracy than its predecessor and has the potential for improving high-throughput root phenotyping procedures based on X-ray computed tomography data analysis. |
| 546 ## - LANGUAGE NOTE | |
| Language note | Text in English |
| 650 #7 - SUBJECT ADDED ENTRY--TOPICAL TERM | |
| Source of heading or term | AGROVOC |
| 9 (RLIN) | 1755 |
| Topical term or geographic name as entry element | Roots |
| 650 #7 - SUBJECT ADDED ENTRY--TOPICAL TERM | |
| Source of heading or term | AGROVOC |
| 9 (RLIN) | 6509 |
| Topical term or geographic name as entry element | Image analysis |
| 650 #7 - SUBJECT ADDED ENTRY--TOPICAL TERM | |
| Source of heading or term | AGROVOC |
| 9 (RLIN) | 11634 |
| Topical term or geographic name as entry element | Root systems |
| 650 #7 - SUBJECT ADDED ENTRY--TOPICAL TERM | |
| Source of heading or term | AGROVOC |
| 9 (RLIN) | 9574 |
| Topical term or geographic name as entry element | X-ray spectroscopy |
| 700 1# - ADDED ENTRY--PERSONAL NAME | |
| 9 (RLIN) | 22449 |
| Personal name | Lippold, E. |
| 700 1# - ADDED ENTRY--PERSONAL NAME | |
| 9 (RLIN) | 22450 |
| Personal name | Vetterlein, D. |
| 700 1# - ADDED ENTRY--PERSONAL NAME | |
| 9 (RLIN) | 22451 |
| Personal name | Schlüter, S. |
| 773 0# - HOST ITEM ENTRY | |
| Place, publisher, and date of publication | London (United Kingdom) : BioMed Central, 2021. |
| Related parts | v. 17, art. 39 |
| Title | Plant Methods |
| Record control number | 57210 |
| International Standard Serial Number | 1746-4811 |
| 856 4# - ELECTRONIC LOCATION AND ACCESS | |
| Link text | Click here to access online |
| Uniform Resource Identifier | https://doi.org/10.1186/s13007-021-00735-4 |
| 942 ## - ADDED ENTRY ELEMENTS (KOHA) | |
| Source of classification or shelving scheme | Dewey Decimal Classification |
| Koha item type | Article |
| Suppress in OPAC | No |
| Date last seen | Total Checkouts | Price effective from | Koha item type | Lost status | Source of classification or shelving scheme | Damaged status | Not for loan | Collection code | Withdrawn status | Home library | Current library | Date acquired |
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 08/25/2021 | 08/25/2021 | Article | Not Lost | Dewey Decimal Classification | Reprints Collection | CIMMYT Knowledge Center: John Woolston Library | CIMMYT Knowledge Center: John Woolston Library | 08/25/2021 |