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  • Automatic Separation of Worm Eggs From Soil and Counting Them Using Lensless Micros

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    Santosh Pandey
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    To assess the severity of nematode infestations in the field, cysts (dead females) of the nematode must be extracted from soil samples and then ground to extract the eggs within. Sucrose centrifugation commonly is used to separate debris from suspensions of extracted nematode eggs. We present a method using OptiPrep as a density gradient medium with improved separation and recovery of extracted eggs compared to the sucrose centrifugation technique.

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    Automatic Separation of Worm Eggs from Soil and Counting them using Lensless Microscopy

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    To assess the severity of nematode infestations in the field, cysts (dead females) of the nematode must be extracted from soil samples and then ground to extract the eggs within. Sucrose centrifugation commonly is used to separate debris from suspensions of extracted nematode eggs. We present a method using OptiPrep as a density gradient medium with improved separation and recovery of extracted eggs compared to the sucrose centrifugation technique.

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    6 views10 pages

    Automatic Separation of Worm Eggs From Soil and Counting Them Using Lensless Micros

    Uploaded by

    Santosh Pandey
    To assess the severity of nematode infestations in the field, cysts (dead females) of the nematode must be extracted from soil samples and then ground to extract the eggs within. Sucrose centrifugation commonly is used to separate debris from suspensions of extracted nematode eggs. We present a method using OptiPrep as a density gradient medium with improved separation and recovery of extracted eggs compared to the sucrose centrifugation technique.

    Copyright:

    Attribution (BY)
    Download as PPT, PDF, TXT or read online from Scribd
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    of 10

    Fig 1. Overview of the new methods of soil sample cleaning and egg counting.

    Kalwa U, Legner C, Wlezien E, Tylka G, Pandey S (2019) New methods of removing debris and
    high-throughput counting of cyst nematode eggs extracted from field soil. PLOS ONE 14(10):
    e0223386. https://doi.org/10.1371/journal.pone.0223386
    https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0223386
    Fig 2. The convolutional autoencoder network model.

    Kalwa U, Legner C, Wlezien E, Tylka G, Pandey S (2019) New methods of removing debris and high-throughput
    counting of cyst nematode eggs extracted from field soil. PLOS ONE 14(10): e0223386.
    https://doi.org/10.1371/journal.pone.0223386
    https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0223386
    Fig 3. Wiring diagram for lensless imaging and design of the microfluidic flow chip.

    Kalwa U, Legner C, Wlezien E, Tylka G, Pandey S (2019) New methods of removing debris and high-throughput
    counting of cyst nematode eggs extracted from field soil. PLOS ONE 14(10): e0223386.
    https://doi.org/10.1371/journal.pone.0223386
    https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0223386
    Fig 4. The algorithm for the lensless SCN egg counting method is depicted as a flow chart.

    Kalwa U, Legner C, Wlezien E, Tylka G, Pandey S (2019) New methods of removing debris and
    high-throughput counting of cyst nematode eggs extracted from field soil. PLOS ONE 14(10):
    e0223386. https://doi.org/10.1371/journal.pone.0223386
    https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0223386
    Fig 5. Distribution of debris in the OptiPrep™ solution before and after centrifugation.

    Kalwa U, Legner C, Wlezien E, Tylka G, Pandey S (2019) New methods of removing debris and
    high-throughput counting of cyst nematode eggs extracted from field soil. PLOS ONE 14(10):
    e0223386. https://doi.org/10.1371/journal.pone.0223386
    https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0223386
    Fig 6. Software program to automatically detect SCN eggs among the debris in the scanner-
    based method.

    Kalwa U, Legner C, Wlezien E, Tylka G, Pandey S (2019) New methods of removing debris and high-throughput counting of cyst
    nematode eggs extracted from field soil. PLOS ONE 14(10): e0223386. https://doi.org/10.1371/journal.pone.0223386
    https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0223386
    Fig 7. Sample cleaning using OptiPrep™ and SCN egg recovery from the three layers.

    Kalwa U, Legner C, Wlezien E, Tylka G, Pandey S (2019) New methods of removing debris and
    high-throughput counting of cyst nematode eggs extracted from field soil. PLOS ONE 14(10):
    e0223386. https://doi.org/10.1371/journal.pone.0223386
    https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0223386
    Fig 8. Comparison of the sample cleaning and SCN egg counting methods.

    Kalwa U, Legner C, Wlezien E, Tylka G, Pandey S (2019) New methods of removing debris and
    high-throughput counting of cyst nematode eggs extracted from field soil. PLOS ONE 14(10):
    e0223386. https://doi.org/10.1371/journal.pone.0223386
    https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0223386
    Fig 9. Reconstruction of the holographic videos and a time-lapsed visualization of the lensless
    imaging method.

    Kalwa U, Legner C, Wlezien E, Tylka G, Pandey S (2019) New methods of removing debris and
    high-throughput counting of cyst nematode eggs extracted from field soil. PLOS ONE 14(10):
    e0223386. https://doi.org/10.1371/journal.pone.0223386
    https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0223386
    Fig 10. Performance of the software programs for automated SCN egg counting.

    Kalwa U, Legner C, Wlezien E, Tylka G, Pandey S (2019) New methods of removing debris and
    high-throughput counting of cyst nematode eggs extracted from field soil. PLOS ONE 14(10):
    e0223386. https://doi.org/10.1371/journal.pone.0223386
    https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0223386

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