Lensfree Fluorescent On-Chip Imaging of Transgenic Caenorhabditis elegans Over an Ultra-Wide Field-of-View
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{"title"=>"Lensfree fluorescent on-chip imaging of transgenic Caenorhabditis elegans over an ultra-wide field-of-view", "type"=>"journal", "authors"=>[{"first_name"=>"Ahmet F.", "last_name"=>"Coskun", "scopus_author_id"=>"35885260000"}, {"first_name"=>"Ikbal", "last_name"=>"Sencan", "scopus_author_id"=>"35280775200"}, {"first_name"=>"Ting Wei", "last_name"=>"Su", "scopus_author_id"=>"35304178700"}, {"first_name"=>"Aydogan", "last_name"=>"Ozcan", "scopus_author_id"=>"7005667692"}], "year"=>2011, "source"=>"PLoS ONE", "identifiers"=>{"pmid"=>"21253611", "doi"=>"10.1371/journal.pone.0015955", "sgr"=>"79251555271", "isbn"=>"1932-6203 (Electronic)\\r1932-6203 (Linking)", "scopus"=>"2-s2.0-79251555271", "issn"=>"19326203", "pui"=>"361180111"}, "id"=>"d2138e21-705d-316d-99c1-8ced8f039f5b", "abstract"=>"We demonstrate lensfree on-chip fluorescent imaging of transgenic Caenorhabditis elegans (C. elegans) over an ultra-wide field-of-view (FOV) of e.g., >2-8 cm(2) with a spatial resolution of ∼10 µm. This is the first time that a lensfree on-chip platform has successfully imaged fluorescent C. elegans samples. In our wide-field lensfree imaging platform, the transgenic samples are excited using a prism interface from the side, where the pump light is rejected through total internal reflection occurring at the bottom facet of the substrate. The emitted fluorescent signal from C. elegans samples is then recorded on a large area opto-electronic sensor-array over an FOV of e.g., >2-8 cm(2), without the use of any lenses, thin-film interference filters or mechanical scanners. Because fluorescent emission rapidly diverges, such lensfree fluorescent images recorded on a chip look blurred due to broad point-spread-function of our platform. To combat this resolution challenge, we use a compressive sampling algorithm to uniquely decode the recorded lensfree fluorescent patterns into higher resolution images, demonstrating ∼10 µm resolution. We tested the efficacy of this compressive decoding approach with different types of opto-electronic sensors to achieve a similar resolution level, independent of the imaging chip. We further demonstrate that this wide FOV lensfree fluorescent imaging platform can also perform sequential bright-field imaging of the same samples using partially-coherent lensfree digital in-line holography that is coupled from the top facet of the same prism used in fluorescent excitation. This unique combination permits ultra-wide field dual-mode imaging of C. elegans on a chip which could especially provide a useful tool for high-throughput screening applications in biomedical research.", "link"=>"http://www.mendeley.com/research/lensfree-fluorescent-onchip-imaging-transgenic-caenorhabditis-elegans-ultrawide-fieldofview", "reader_count"=>65, "reader_count_by_academic_status"=>{"Unspecified"=>2, "Professor > Associate Professor"=>3, "Researcher"=>22, "Student > Doctoral Student"=>3, "Student > Ph. D. Student"=>16, "Student > Postgraduate"=>3, "Student > Master"=>10, "Other"=>2, "Student > Bachelor"=>2, "Lecturer > Senior Lecturer"=>1, "Professor"=>1}, "reader_count_by_user_role"=>{"Unspecified"=>2, "Professor > Associate Professor"=>3, "Researcher"=>22, "Student > Doctoral Student"=>3, "Student > Ph. D. Student"=>16, "Student > Postgraduate"=>3, "Student > Master"=>10, "Other"=>2, "Student > Bachelor"=>2, "Lecturer > Senior Lecturer"=>1, "Professor"=>1}, "reader_count_by_subject_area"=>{"Engineering"=>32, "Unspecified"=>2, "Biochemistry, Genetics and Molecular Biology"=>1, "Materials Science"=>1, "Agricultural and Biological Sciences"=>15, "Neuroscience"=>1, "Chemical Engineering"=>1, "Physics and Astronomy"=>9, "Chemistry"=>2, "Immunology and Microbiology"=>1}, "reader_count_by_subdiscipline"=>{"Engineering"=>{"Engineering"=>32}, "Materials Science"=>{"Materials Science"=>1}, "Neuroscience"=>{"Neuroscience"=>1}, "Chemistry"=>{"Chemistry"=>2}, "Physics and Astronomy"=>{"Physics and Astronomy"=>9}, "Immunology and Microbiology"=>{"Immunology and Microbiology"=>1}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>15}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>1}, "Unspecified"=>{"Unspecified"=>2}, "Chemical Engineering"=>{"Chemical Engineering"=>1}}, "reader_count_by_country"=>{"Netherlands"=>1, "Belgium"=>1, "United States"=>7, "Japan"=>2, "United Kingdom"=>1, "South Africa"=>1, "Switzerland"=>1}, "group_count"=>2}

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/808497"], "description"=>"<p>Lensfree on-chip fluorescent imaging of transgenic <i>C. elegans</i> is shown for three individual animals using KAF-8300 sensor. (a4), (b4) and (c4) illustrate the lensfree fluorescent raw images that all look blurry at the detector plane. Compressive decoding of these blurry patterns enabled digital reconstruction of much higher resolution fluorescent images of these <i>C. elegans</i> samples as shown in (a5), (b5) and (c5), respectively. 10× objective-lens fluorescent microscope images of the same worms shown in (a2), (b2) and (c2) agree well with our decoded lensfree fluorescent images. In addition to fluorescent imaging, the same lensfree platform also permits holographic <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0015955#pone.0015955-Isikman1\" target=\"_blank\">[18]</a> transmission imaging of the same samples such that hybrid images can be created by superimposing the decoded lensfree fluorescent images and the reconstructed holographic images as shown in (a6), (b6) and (c6). Microscope comparisons of the same samples are also provided in (a3), (b3) and (c3), respectively. Slight rotations of the worms are observed between the lensfree decoded images and their microscope comparison images since they are acquired at different experiments.</p>", "links"=>[], "tags"=>["fluorescent", "holographic", "imaging"], "article_id"=>478864, "categories"=>["Information And Computing Sciences", "Biotechnology", "Physics"], "users"=>["Ahmet F. Coskun", "Ikbal Sencan", "Ting-Wei Su", "Aydogan Ozcan"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0015955.g004", "stats"=>{"downloads"=>1, "page_views"=>3, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Lensfree_fluorescent_and_holographic_transmission_imaging_of_C_elegans_/478864", "title"=>"Lensfree fluorescent and holographic transmission imaging of <i>C. elegans</i>.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2011-01-06 02:27:44"}
  • {"files"=>["https://ndownloader.figshare.com/files/808369"], "description"=>"<p>Same as in <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0015955#pone-0015955-g002\" target=\"_blank\">Fig. 2</a>, except for KAF-39000 sensor-chip. Similar to <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0015955#pone-0015955-g002\" target=\"_blank\">Fig. 2</a>, compressive decoding enables a lensfree spatial resolution of ∼10 µm on a chip. Because of its different sensor design, the measured PSF of KAF-39000 is quite different than the PSF of KAF-8300 shown in <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0015955#pone-0015955-g002\" target=\"_blank\">Fig. 2</a>. This, however, does <b><i>not</i></b> pose a limitation for achieving a similar spatial resolution. These experimental results, together with <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0015955#pone-0015955-g002\" target=\"_blank\">Fig. 2</a>, successfully demonstrate the sensor-chip independent decoding performance of our lensfree fluorescent imaging platform.</p>", "links"=>[], "tags"=>["lensfree", "fluorescent", "imaging"], "article_id"=>478737, "categories"=>["Information And Computing Sciences", "Biotechnology", "Physics"], "users"=>["Ahmet F. Coskun", "Ikbal Sencan", "Ting-Wei Su", "Aydogan Ozcan"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0015955.g003", "stats"=>{"downloads"=>4, "page_views"=>8, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Decoding_performance_of_our_lensfree_fluorescent_imaging_platform_with_a_different_sensor_chip_/478737", "title"=>"Decoding performance of our lensfree fluorescent imaging platform with a different sensor chip.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2011-01-06 02:25:37"}
  • {"files"=>["https://ndownloader.figshare.com/files/808598"], "description"=>"<p>Same as in <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0015955#pone-0015955-g004\" target=\"_blank\">Fig. 4</a>, except this time for a different sensor chip (KAF-11002; 9µm pixel size, 11 MPixel). Similar to <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0015955#pone-0015955-g004\" target=\"_blank\">Fig. 4</a>, the decoded lensfree fluorescent image of the transgenic <i>C. elegans</i> sample provides a decent match to a conventional fluorescent microscope image of the same worm (acquired with a 10× objective-lens, NA = 0.25). Slight rotation of the worm is observed between the lensfree decoded image and its microscope comparison image since the two are acquired at different experiments.</p>", "links"=>[], "tags"=>["imaging", "transgenic"], "article_id"=>478969, "categories"=>["Information And Computing Sciences", "Biotechnology", "Physics"], "users"=>["Ahmet F. Coskun", "Ikbal Sencan", "Ting-Wei Su", "Aydogan Ozcan"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0015955.g005", "stats"=>{"downloads"=>2, "page_views"=>2, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Lensfree_imaging_of_transgenic_C_elegans_with_a_different_sensor_chip_/478969", "title"=>"Lensfree imaging of transgenic <i>C. elegans</i> with a different sensor chip.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2011-01-06 02:29:29"}
  • {"files"=>["https://ndownloader.figshare.com/files/808231"], "description"=>"<p>(Top Row) illustrates wide-field lensfree fluorescent imaging results for 4 µm fluorescent beads recorded using KAF-8300 sensor. The <i>measured</i> point-spread-function (PSF) of the same system (corresponding to 4 µm diameter fluorescent beads) is also shown at the top left. The 2D pattern of this PSF presents a <i>unique</i> signature, which is mostly dictated by the opto-electronic design of the CCD chip. (Middle and Bottom Rows) Lensfree fluorescent images of various 4 µm bead-pairs are shown. For comparison purposes, the inset images in each frame also show conventional fluorescent microscope images of the same closely-packed beads. Based on these microscope images, the center-to-center distances (<b>d<sub>mic</sub></b>) between the fluorescent particles are calculated. Using compressive sampling (CS - as indicated with the solid black arrows), lensfree fluorescent raw images are decoded to resolve the individual fluorescent particles from each other. These decoding results nicely match to the corresponding microscope comparison images for <b>d<sub>mic</sub></b>≥10µm, indicating a resolution of ∼10µm. <b>d<sub>CS</sub></b> refers to the center-to-center distances of these resolved fluorescent particles in the decoded lensfree images. For <b>d<sub>mic</sub></b> = 6µm case, however, compressive decoding does not succeed in resolving the particles.</p>", "links"=>[], "tags"=>["fluorescent", "images"], "article_id"=>478601, "categories"=>["Information And Computing Sciences", "Biotechnology", "Physics"], "users"=>["Ahmet F. Coskun", "Ikbal Sencan", "Ting-Wei Su", "Aydogan Ozcan"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0015955.g002", "stats"=>{"downloads"=>1, "page_views"=>3, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Lensfree_fluorescent_images_of_various_4_181_m_bead_pairs_/478601", "title"=>"Lensfree fluorescent images of various 4 µm bead-pairs.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2011-01-06 02:23:21"}
  • {"files"=>["https://ndownloader.figshare.com/files/808096"], "description"=>"<p>(a) Schematic diagram of lensfree on-chip fluorescent and holographic imaging platform is shown. Fluorescent excitation is achieved through the side facet of a rhomboid prism using an incoherent source (i.e. spectrally filtered Xenon lamp); and holographic illumination is achieved through the top facet of the same prism using an LED (632 nm peak, and ∼20 nm bandwidth). (b) Lensfree fluorescent imaging is demonstrated over >2 cm<sup>2</sup> using KAF-8300 sensor (Full Frame CCD with a pixel size of 5.4 µm). (c) shows the experimental set-up of lensfree fluorescent imaging platform for the same sensor. The fluorescent <i>C. elegans</i> samples were excited through a prism interface, where an index matching oil was used to assemble the chip and the prism. Only the fluorescent emission emerging from gene-expressed parts of the worm body is detected by the KAF-8300 sensor-chip. (d) On-chip lensfree fluorescent imaging is illustrated over >8cm<sup>2</sup> using KAF-39000 sensor (Full Frame CCD with a pixel size of 6.8 µm). (e) shows the experimental set-up of lensfree fluorescent imaging platform for the same sensor. Note that the excitation source in both of these set-ups is tunable, and therefore various fluorescent dyes could potentially be used without an issue.</p>", "links"=>[], "tags"=>["on-chip", "fluorescent", "holographic", "imaging"], "article_id"=>478460, "categories"=>["Information And Computing Sciences", "Biotechnology", "Physics"], "users"=>["Ahmet F. Coskun", "Ikbal Sencan", "Ting-Wei Su", "Aydogan Ozcan"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0015955.g001", "stats"=>{"downloads"=>1, "page_views"=>1, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Lensfree_on_chip_fluorescent_and_holographic_imaging_platform_/478460", "title"=>"Lensfree on-chip fluorescent and holographic imaging platform.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2011-01-06 02:21:00"}
  • {"files"=>["https://ndownloader.figshare.com/files/403273", "https://ndownloader.figshare.com/files/403277", "https://ndownloader.figshare.com/files/403283", "https://ndownloader.figshare.com/files/403294", "https://ndownloader.figshare.com/files/403297"], "description"=>"<div><p>We demonstrate lensfree on-chip fluorescent imaging of transgenic <em>Caenorhabditis elegans</em> (<em>C. elegans</em>) over an ultra-wide field-of-view (FOV) of e.g., >2–8 cm<sup>2</sup> with a spatial resolution of ∼10µm. This is the first time that a lensfree on-chip platform has successfully imaged fluorescent <em>C. elegans</em> samples. In our wide-field lensfree imaging platform, the transgenic samples are excited using a prism interface from the side, where the pump light is rejected through total internal reflection occurring at the bottom facet of the substrate. The emitted fluorescent signal from <em>C. elegans</em> samples is then recorded on a large area opto-electronic sensor-array over an FOV of e.g., >2–8 cm<sup>2</sup>, without the use of any lenses, thin-film interference filters or mechanical scanners. Because fluorescent emission rapidly diverges, such lensfree fluorescent images recorded on a chip look blurred due to broad point-spread-function of our platform. To combat this resolution challenge, we use a compressive sampling algorithm to uniquely decode the recorded lensfree fluorescent patterns into higher resolution images, demonstrating ∼10 µm resolution. We tested the efficacy of this compressive decoding approach with different types of opto-electronic sensors to achieve a similar resolution level, independent of the imaging chip. We further demonstrate that this wide FOV lensfree fluorescent imaging platform can also perform sequential bright-field imaging of the same samples using partially-coherent lensfree digital in-line holography that is coupled from the top facet of the same prism used in fluorescent excitation. This unique combination permits ultra-wide field dual-mode imaging of <em>C. elegans</em> on a chip which could especially provide a useful tool for high-throughput screening applications in biomedical research.</p> </div>", "links"=>[], "tags"=>["lensfree", "fluorescent", "on-chip", "imaging", "transgenic", "ultra-wide", "field-of-view"], "article_id"=>139678, "categories"=>["Information And Computing Sciences", "Biotechnology", "Physics"], "users"=>["Ahmet F. Coskun", "Ikbal Sencan", "Ting-Wei Su", "Aydogan Ozcan"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0015955.s001", "https://dx.doi.org/10.1371/journal.pone.0015955.s002", "https://dx.doi.org/10.1371/journal.pone.0015955.s003", "https://dx.doi.org/10.1371/journal.pone.0015955.s004", "https://dx.doi.org/10.1371/journal.pone.0015955.s005"], "stats"=>{"downloads"=>12, "page_views"=>13, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/Lensfree_Fluorescent_On_Chip_Imaging_of_Transgenic_Caenorhabditis_elegans_Over_an_Ultra_Wide_Field_of_View/139678", "title"=>"Lensfree Fluorescent On-Chip Imaging of Transgenic <em>Caenorhabditis elegans</em> Over an Ultra-Wide Field-of-View", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2011-01-06 02:41:18"}

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Relative Metric

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