Segmentation and characterization of macerated fibers and vessels using deep learning. Qamar, S., Baba, A. I., Verger, S., & Andersson, M. Plant Methods, 20(1):126, August, 2024. ![Segmentation and characterization of macerated fibers and vessels using deep learning [link]](https://bibbase.org/img/filetypes/link.svg "link")
Paper doi abstract bibtex Abstract Purpose Wood comprises different cell types, such as fibers, tracheids and vessels, defining its properties. Studying cells’ shape, size, and arrangement in microscopy images is crucial for understanding wood characteristics. Typically, this involves macerating (soaking) samples in a solution to separate cells, then spreading them on slides for imaging with a microscope that covers a wide area, capturing thousands of cells. However, these cells often cluster and overlap in images, making the segmentation difficult and time-consuming using standard image-processing methods. Results In this work, we developed an automatic deep learning segmentation approach that utilizes the one-stage YOLOv8 model for fast and accurate segmentation and characterization of macerated fiber and vessel form aspen trees in microscopy images. The model can analyze 32,640 x 25,920 pixels images and demonstrate effective cell detection and segmentation, achieving a $$\hbox \mAP\_\0.5-0.95\$$ mAP 0.5 - 0.95 of 78 %. To assess the model’s robustness, we examined fibers from a genetically modified tree line known for longer fibers. The outcomes were comparable to previous manual measurements. Additionally, we created a user-friendly web application for image analysis and provided the code for use on Google Colab. Conclusion By leveraging YOLOv8’s advances, this work provides a deep learning solution to enable efficient quantification and analysis of wood cells suitable for practical applications.
@article{qamar_segmentation_2024,
title = {Segmentation and characterization of macerated fibers and vessels using deep learning},
volume = {20},
issn = {1746-4811},
url = {https://plantmethods.biomedcentral.com/articles/10.1186/s13007-024-01244-w},
doi = {10.1186/s13007-024-01244-w},
abstract = {Abstract
Purpose
Wood comprises different cell types, such as fibers, tracheids and vessels, defining its properties. Studying cells’ shape, size, and arrangement in microscopy images is crucial for understanding wood characteristics. Typically, this involves macerating (soaking) samples in a solution to separate cells, then spreading them on slides for imaging with a microscope that covers a wide area, capturing thousands of cells. However, these cells often cluster and overlap in images, making the segmentation difficult and time-consuming using standard image-processing methods.
Results
In this work, we developed an automatic deep learning segmentation approach that utilizes the one-stage YOLOv8 model for fast and accurate segmentation and characterization of macerated fiber and vessel form aspen trees in microscopy images. The model can analyze 32,640 x 25,920 pixels images and demonstrate effective cell detection and segmentation, achieving a
\$\${\textbackslash}hbox \{mAP\}\_\{0.5-0.95\}\$\$
mAP
0.5
-
0.95
of 78 \%. To assess the model’s robustness, we examined fibers from a genetically modified tree line known for longer fibers. The outcomes were comparable to previous manual measurements. Additionally, we created a user-friendly web application for image analysis and provided the code for use on Google Colab.
Conclusion
By leveraging YOLOv8’s advances, this work provides a deep learning solution to enable efficient quantification and analysis of wood cells suitable for practical applications.},
language = {en},
number = {1},
urldate = {2024-08-30},
journal = {Plant Methods},
author = {Qamar, Saqib and Baba, Abu Imran and Verger, Stéphane and Andersson, Magnus},
month = aug,
year = {2024},
pages = {126},
}
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{"_id":"yL8vAtthEMP9ZsbnS","bibbaseid":"qamar-baba-verger-andersson-segmentationandcharacterizationofmaceratedfibersandvesselsusingdeeplearning-2024","author_short":["Qamar, S.","Baba, A. I.","Verger, S.","Andersson, M."],"bibdata":{"bibtype":"article","type":"article","title":"Segmentation and characterization of macerated fibers and vessels using deep learning","volume":"20","issn":"1746-4811","url":"https://plantmethods.biomedcentral.com/articles/10.1186/s13007-024-01244-w","doi":"10.1186/s13007-024-01244-w","abstract":"Abstract Purpose Wood comprises different cell types, such as fibers, tracheids and vessels, defining its properties. Studying cells’ shape, size, and arrangement in microscopy images is crucial for understanding wood characteristics. Typically, this involves macerating (soaking) samples in a solution to separate cells, then spreading them on slides for imaging with a microscope that covers a wide area, capturing thousands of cells. However, these cells often cluster and overlap in images, making the segmentation difficult and time-consuming using standard image-processing methods. Results In this work, we developed an automatic deep learning segmentation approach that utilizes the one-stage YOLOv8 model for fast and accurate segmentation and characterization of macerated fiber and vessel form aspen trees in microscopy images. The model can analyze 32,640 x 25,920 pixels images and demonstrate effective cell detection and segmentation, achieving a $$\\hbox \\mAP\\_\\0.5-0.95\\$$ mAP 0.5 - 0.95 of 78 %. To assess the model’s robustness, we examined fibers from a genetically modified tree line known for longer fibers. The outcomes were comparable to previous manual measurements. Additionally, we created a user-friendly web application for image analysis and provided the code for use on Google Colab. Conclusion By leveraging YOLOv8’s advances, this work provides a deep learning solution to enable efficient quantification and analysis of wood cells suitable for practical applications.","language":"en","number":"1","urldate":"2024-08-30","journal":"Plant Methods","author":[{"propositions":[],"lastnames":["Qamar"],"firstnames":["Saqib"],"suffixes":[]},{"propositions":[],"lastnames":["Baba"],"firstnames":["Abu","Imran"],"suffixes":[]},{"propositions":[],"lastnames":["Verger"],"firstnames":["Stéphane"],"suffixes":[]},{"propositions":[],"lastnames":["Andersson"],"firstnames":["Magnus"],"suffixes":[]}],"month":"August","year":"2024","pages":"126","bibtex":"@article{qamar_segmentation_2024,\n\ttitle = {Segmentation and characterization of macerated fibers and vessels using deep learning},\n\tvolume = {20},\n\tissn = {1746-4811},\n\turl = {https://plantmethods.biomedcentral.com/articles/10.1186/s13007-024-01244-w},\n\tdoi = {10.1186/s13007-024-01244-w},\n\tabstract = {Abstract\n \n Purpose\n Wood comprises different cell types, such as fibers, tracheids and vessels, defining its properties. Studying cells’ shape, size, and arrangement in microscopy images is crucial for understanding wood characteristics. Typically, this involves macerating (soaking) samples in a solution to separate cells, then spreading them on slides for imaging with a microscope that covers a wide area, capturing thousands of cells. However, these cells often cluster and overlap in images, making the segmentation difficult and time-consuming using standard image-processing methods.\n \n \n Results\n \n In this work, we developed an automatic deep learning segmentation approach that utilizes the one-stage YOLOv8 model for fast and accurate segmentation and characterization of macerated fiber and vessel form aspen trees in microscopy images. The model can analyze 32,640 x 25,920 pixels images and demonstrate effective cell detection and segmentation, achieving a\n \n \n \\$\\${\\textbackslash}hbox \\{mAP\\}\\_\\{0.5-0.95\\}\\$\\$\n \n \n mAP\n \n 0.5\n -\n 0.95\n \n \n \n \n \n of 78 \\%. To assess the model’s robustness, we examined fibers from a genetically modified tree line known for longer fibers. The outcomes were comparable to previous manual measurements. Additionally, we created a user-friendly web application for image analysis and provided the code for use on Google Colab.\n \n \n \n Conclusion\n By leveraging YOLOv8’s advances, this work provides a deep learning solution to enable efficient quantification and analysis of wood cells suitable for practical applications.},\n\tlanguage = {en},\n\tnumber = {1},\n\turldate = {2024-08-30},\n\tjournal = {Plant Methods},\n\tauthor = {Qamar, Saqib and Baba, Abu Imran and Verger, Stéphane and Andersson, Magnus},\n\tmonth = aug,\n\tyear = {2024},\n\tpages = {126},\n}\n\n\n\n\n\n\n\n","author_short":["Qamar, S.","Baba, A. I.","Verger, S.","Andersson, M."],"key":"qamar_segmentation_2024","id":"qamar_segmentation_2024","bibbaseid":"qamar-baba-verger-andersson-segmentationandcharacterizationofmaceratedfibersandvesselsusingdeeplearning-2024","role":"author","urls":{"Paper":"https://plantmethods.biomedcentral.com/articles/10.1186/s13007-024-01244-w"},"metadata":{"authorlinks":{}}},"bibtype":"article","biburl":"https://bibbase.org/zotero/upscpub","dataSources":["3zTPPmKj8BiTcpc6C","9cGcv2t8pRzC92kzs"],"keywords":[],"search_terms":["segmentation","characterization","macerated","fibers","vessels","using","deep","learning","qamar","baba","verger","andersson"],"title":"Segmentation and characterization of macerated fibers and vessels using deep learning","year":2024}