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microscope platform  (Mad City Labs)


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    Structured Review

    Mad City Labs microscope platform
    A Schematic of the nanofluidic chip used. B Zoom-in on the nanofluidic part of the chip depicting the microfluidic inlet and outlet channels that connect to liquid reservoirs used to interface the chip holder and to a set of parallel nanofluidic channels used for NSM experiments. The length of the nanochannels is chosen such that they fit the field of view of the <t>microscope</t> at the desired magnification, and the cross-section of the nanochannels is tailored to the size of the molecule to be analyzed, as discussed in the main text. The two indicated channel dimensions correspond to the two nanochannel types used in the experiment depicted in ( D ). C The principle of differential imaging in NSM, in which we subtract the light scattered (yellow arrows indicate the scattered-light direction) by an empty nanochannel from the light scattered by the same channel with a molecule inside. A sequence of differential images of a nanochannel containing a diffusing single molecule obtained in this way is combined into a kymograph in ( D ), which then contains the full molecular trajectory. Here, this is exemplified for a Bovine Serum Albumin (BSA, MW = 66.8 kDa, R s = 3.5 nm) molecule differentially imaged in two nanochannels with different cross sections (defined by the widest and deepest points of the cross sections; see insets for cross-section scanning electron microscope images), i.e., and A I I I = 153nm × 32nm and A I V = 118nm × 30nm. While the trajectory of the BSA molecule is not resolved for the larger A I I I channel when only applying the standard data preprocessing steps outlined in the Methods section, it is clearly visible in the smaller channel A I V . This showcases the potential of lowering the LoD of NSM by reducing the nanochannel cross section area A , since A is inversely proportional to the LoD . For a more detailed statistical analysis of BSA and its dimeric oligomers, we refer to our seminal NSM work . Here, NSM denotes nanofluidic scattering microscopy, BSA bovine serum albumin, MW molecular weight, R s hydrodynamic radius, and LoD limit of detection.
    Microscope Platform, supplied by Mad City Labs, used in various techniques. Bioz Stars score: 94/100, based on 67 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    94/100 stars

    Images

    1) Product Images from "Label-free mass and size characterization of few-kDa biomolecules by hierarchical vision transformer augmented nanofluidic scattering microscopy"

    Article Title: Label-free mass and size characterization of few-kDa biomolecules by hierarchical vision transformer augmented nanofluidic scattering microscopy

    Journal: Nature Communications

    doi: 10.1038/s41467-026-70514-z

    A Schematic of the nanofluidic chip used. B Zoom-in on the nanofluidic part of the chip depicting the microfluidic inlet and outlet channels that connect to liquid reservoirs used to interface the chip holder and to a set of parallel nanofluidic channels used for NSM experiments. The length of the nanochannels is chosen such that they fit the field of view of the microscope at the desired magnification, and the cross-section of the nanochannels is tailored to the size of the molecule to be analyzed, as discussed in the main text. The two indicated channel dimensions correspond to the two nanochannel types used in the experiment depicted in ( D ). C The principle of differential imaging in NSM, in which we subtract the light scattered (yellow arrows indicate the scattered-light direction) by an empty nanochannel from the light scattered by the same channel with a molecule inside. A sequence of differential images of a nanochannel containing a diffusing single molecule obtained in this way is combined into a kymograph in ( D ), which then contains the full molecular trajectory. Here, this is exemplified for a Bovine Serum Albumin (BSA, MW = 66.8 kDa, R s = 3.5 nm) molecule differentially imaged in two nanochannels with different cross sections (defined by the widest and deepest points of the cross sections; see insets for cross-section scanning electron microscope images), i.e., and A I I I = 153nm × 32nm and A I V = 118nm × 30nm. While the trajectory of the BSA molecule is not resolved for the larger A I I I channel when only applying the standard data preprocessing steps outlined in the Methods section, it is clearly visible in the smaller channel A I V . This showcases the potential of lowering the LoD of NSM by reducing the nanochannel cross section area A , since A is inversely proportional to the LoD . For a more detailed statistical analysis of BSA and its dimeric oligomers, we refer to our seminal NSM work . Here, NSM denotes nanofluidic scattering microscopy, BSA bovine serum albumin, MW molecular weight, R s hydrodynamic radius, and LoD limit of detection.
    Figure Legend Snippet: A Schematic of the nanofluidic chip used. B Zoom-in on the nanofluidic part of the chip depicting the microfluidic inlet and outlet channels that connect to liquid reservoirs used to interface the chip holder and to a set of parallel nanofluidic channels used for NSM experiments. The length of the nanochannels is chosen such that they fit the field of view of the microscope at the desired magnification, and the cross-section of the nanochannels is tailored to the size of the molecule to be analyzed, as discussed in the main text. The two indicated channel dimensions correspond to the two nanochannel types used in the experiment depicted in ( D ). C The principle of differential imaging in NSM, in which we subtract the light scattered (yellow arrows indicate the scattered-light direction) by an empty nanochannel from the light scattered by the same channel with a molecule inside. A sequence of differential images of a nanochannel containing a diffusing single molecule obtained in this way is combined into a kymograph in ( D ), which then contains the full molecular trajectory. Here, this is exemplified for a Bovine Serum Albumin (BSA, MW = 66.8 kDa, R s = 3.5 nm) molecule differentially imaged in two nanochannels with different cross sections (defined by the widest and deepest points of the cross sections; see insets for cross-section scanning electron microscope images), i.e., and A I I I = 153nm × 32nm and A I V = 118nm × 30nm. While the trajectory of the BSA molecule is not resolved for the larger A I I I channel when only applying the standard data preprocessing steps outlined in the Methods section, it is clearly visible in the smaller channel A I V . This showcases the potential of lowering the LoD of NSM by reducing the nanochannel cross section area A , since A is inversely proportional to the LoD . For a more detailed statistical analysis of BSA and its dimeric oligomers, we refer to our seminal NSM work . Here, NSM denotes nanofluidic scattering microscopy, BSA bovine serum albumin, MW molecular weight, R s hydrodynamic radius, and LoD limit of detection.

    Techniques Used: Microscopy, Imaging, Sequencing, Molecular Weight

    Related Articles

    Incubation:

    Article Title: Structural basis of pH-dependent activation in a CLC transporter.
    Article Snippet: CLCs are dimeric chloride channels and anion/proton exchangers that regulate processes such as muscle contraction and endo-lysosome acidification.. Common gating controls their activity; its closure simultaneously silences both protomers, and its opening allows them to independently transport ions.. Mutations affecting common gating in human CLCs cause dominant genetic disorders.

    Membrane:

    Article Title: Structural basis of pH-dependent activation in a CLC transporter.
    Article Snippet: CLCs are dimeric chloride channels and anion/proton exchangers that regulate processes such as muscle contraction and endo-lysosome acidification.. Common gating controls their activity; its closure simultaneously silences both protomers, and its opening allows them to independently transport ions.. Mutations affecting common gating in human CLCs cause dominant genetic disorders.

    Imaging:

    Article Title: Structural basis of pH-dependent activation in a CLC transporter.
    Article Snippet: CLCs are dimeric chloride channels and anion/proton exchangers that regulate processes such as muscle contraction and endo-lysosome acidification.. Common gating controls their activity; its closure simultaneously silences both protomers, and its opening allows them to independently transport ions.. Mutations affecting common gating in human CLCs cause dominant genetic disorders.

    Article Title: Single-molecule tracking in live Yersinia enterocolitica reveals distinct cytosolic complexes of injectisome subunits.
    Article Snippet: Proteins were separated on 186 Novex 4–20% gradient SDS–PAGE gels and stained using the Coomassie-based ‘Instant blue’ 187 staining solution (Expedeon, San Diego, California), or immunoblotted using rabbit polyclonal 188 antibodies against Y. enterocolitica SctQ (MIPA235; 1:1,000) (Fig. S1). .. 189 190 Super-resolution Fluorescence Imaging 191 Experiments were performed on a custom-built dual-color inverted fluorescence 192 microscope based on the RM21 platform (Mad City Labs, Inc, Madison, Wisconsin). ..

    Article Title: Dimerization of iLID optogenetic proteins observed using 3D single-molecule tracking in live E. coli.
    Article Snippet: 3D single-molecule tracking microscopy has enabled measurements of protein diffusion in living cells, offering information about protein dynamics and cellular environments.. For example, different diffusive states can be resolved and assigned to protein complexes of different size and composition.. However, substantial statistical power and biological validation, often through genetic deletion of binding partners, are required to support diffusive state assignments.

    Article Title: Resolving Cytosolic Diffusive States in Bacteria by Single-Molecule Tracking
    Article Snippet: .. Super-resolution fluorescence imaging setup Experiments were performed on a custom-built dual-color inverted fluorescence microscope based on the RM21 platform (Mad City Labs, Madison, WI). ..

    Fluorescence:

    Article Title: Structural basis of pH-dependent activation in a CLC transporter.
    Article Snippet: CLCs are dimeric chloride channels and anion/proton exchangers that regulate processes such as muscle contraction and endo-lysosome acidification.. Common gating controls their activity; its closure simultaneously silences both protomers, and its opening allows them to independently transport ions.. Mutations affecting common gating in human CLCs cause dominant genetic disorders.

    Article Title: Resolving Cytosolic Diffusive States in Bacteria by Single-Molecule Tracking
    Article Snippet: .. Experiments were performed on a custom-built dual-color inverted fluorescence microscope based on the RM21 platform (Mad City Labs, Madison, WI). ..

    Article Title: Distinct Cytosolic Complexes Containing the Type III Secretion System ATPase Resolved by Three-Dimensional Single-Molecule Tracking in Live Yersinia enterocolitica
    Article Snippet: The immunoblot was visualized using enhanced chemiluminescence (ECL) substrate (Pierce) on a LAS-4000 luminescence image analyzer (Fujifilm). .. Image data were acquired on a custom-built inverted fluorescence microscope based on the RM21 platform (Mad City Labs, Inc, Madison, WI), as previously described ( , ). ..

    Article Title: Distinct complexes containing the cytosolic type III secretion system ATPase resolved by 3D single-molecule tracking in live Yersinia enterocolitica
    Article Snippet: .. Image data were acquired on a custom-built inverted fluorescence microscope based on the RM21 platform (Mad City Labs, Inc, Madison, Wisconsin), as previously described , . ..

    Article Title: Cooperative Binding of Cytosolic Type III Secretion System Proteins to the Injectisome Revealed by Live-Cell Single-Molecule Localization Microscopy
    Article Snippet: .. Image data were acquired on a custom-built inverted fluorescence microscope based on the RM21 platform (Mad City Labs, Madison, WI), as previously described , . ..

    Article Title: Single-molecule tracking in live Yersinia enterocolitica reveals distinct cytosolic complexes of injectisome subunits.
    Article Snippet: Proteins were separated on 186 Novex 4–20% gradient SDS–PAGE gels and stained using the Coomassie-based ‘Instant blue’ 187 staining solution (Expedeon, San Diego, California), or immunoblotted using rabbit polyclonal 188 antibodies against Y. enterocolitica SctQ (MIPA235; 1:1,000) (Fig. S1). .. 189 190 Super-resolution Fluorescence Imaging 191 Experiments were performed on a custom-built dual-color inverted fluorescence 192 microscope based on the RM21 platform (Mad City Labs, Inc, Madison, Wisconsin). ..

    Article Title: Dimerization of iLID optogenetic proteins observed using 3D single-molecule tracking in live E. coli.
    Article Snippet: 3D single-molecule tracking microscopy has enabled measurements of protein diffusion in living cells, offering information about protein dynamics and cellular environments.. For example, different diffusive states can be resolved and assigned to protein complexes of different size and composition.. However, substantial statistical power and biological validation, often through genetic deletion of binding partners, are required to support diffusive state assignments.

    Article Title: Resolving Cytosolic Diffusive States in Bacteria by Single-Molecule Tracking
    Article Snippet: .. Super-resolution fluorescence imaging setup Experiments were performed on a custom-built dual-color inverted fluorescence microscope based on the RM21 platform (Mad City Labs, Madison, WI). ..

    Microscopy:

    Article Title: Structural basis of pH-dependent activation in a CLC transporter.
    Article Snippet: CLCs are dimeric chloride channels and anion/proton exchangers that regulate processes such as muscle contraction and endo-lysosome acidification.. Common gating controls their activity; its closure simultaneously silences both protomers, and its opening allows them to independently transport ions.. Mutations affecting common gating in human CLCs cause dominant genetic disorders.

    Article Title: Resolving Cytosolic Diffusive States in Bacteria by Single-Molecule Tracking
    Article Snippet: .. Experiments were performed on a custom-built dual-color inverted fluorescence microscope based on the RM21 platform (Mad City Labs, Madison, WI). ..

    Article Title: Distinct Cytosolic Complexes Containing the Type III Secretion System ATPase Resolved by Three-Dimensional Single-Molecule Tracking in Live Yersinia enterocolitica
    Article Snippet: The immunoblot was visualized using enhanced chemiluminescence (ECL) substrate (Pierce) on a LAS-4000 luminescence image analyzer (Fujifilm). .. Image data were acquired on a custom-built inverted fluorescence microscope based on the RM21 platform (Mad City Labs, Inc, Madison, WI), as previously described ( , ). ..

    Article Title: Distinct complexes containing the cytosolic type III secretion system ATPase resolved by 3D single-molecule tracking in live Yersinia enterocolitica
    Article Snippet: .. Image data were acquired on a custom-built inverted fluorescence microscope based on the RM21 platform (Mad City Labs, Inc, Madison, Wisconsin), as previously described , . ..

    Article Title: Cooperative Binding of Cytosolic Type III Secretion System Proteins to the Injectisome Revealed by Live-Cell Single-Molecule Localization Microscopy
    Article Snippet: .. Image data were acquired on a custom-built inverted fluorescence microscope based on the RM21 platform (Mad City Labs, Madison, WI), as previously described , . ..

    Article Title: Single-molecule tracking in live Yersinia enterocolitica reveals distinct cytosolic complexes of injectisome subunits.
    Article Snippet: Proteins were separated on 186 Novex 4–20% gradient SDS–PAGE gels and stained using the Coomassie-based ‘Instant blue’ 187 staining solution (Expedeon, San Diego, California), or immunoblotted using rabbit polyclonal 188 antibodies against Y. enterocolitica SctQ (MIPA235; 1:1,000) (Fig. S1). .. 189 190 Super-resolution Fluorescence Imaging 191 Experiments were performed on a custom-built dual-color inverted fluorescence 192 microscope based on the RM21 platform (Mad City Labs, Inc, Madison, Wisconsin). ..

    Article Title: Dimerization of iLID optogenetic proteins observed using 3D single-molecule tracking in live E. coli.
    Article Snippet: 3D single-molecule tracking microscopy has enabled measurements of protein diffusion in living cells, offering information about protein dynamics and cellular environments.. For example, different diffusive states can be resolved and assigned to protein complexes of different size and composition.. However, substantial statistical power and biological validation, often through genetic deletion of binding partners, are required to support diffusive state assignments.

    Article Title: Resolving Cytosolic Diffusive States in Bacteria by Single-Molecule Tracking
    Article Snippet: .. Super-resolution fluorescence imaging setup Experiments were performed on a custom-built dual-color inverted fluorescence microscope based on the RM21 platform (Mad City Labs, Madison, WI). ..



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    A Schematic of the nanofluidic chip used. B Zoom-in on the nanofluidic part of the chip depicting the microfluidic inlet and outlet channels that connect to liquid reservoirs used to interface the chip holder and to a set of parallel nanofluidic channels used for NSM experiments. The length of the nanochannels is chosen such that they fit the field of view of the <t>microscope</t> at the desired magnification, and the cross-section of the nanochannels is tailored to the size of the molecule to be analyzed, as discussed in the main text. The two indicated channel dimensions correspond to the two nanochannel types used in the experiment depicted in ( D ). C The principle of differential imaging in NSM, in which we subtract the light scattered (yellow arrows indicate the scattered-light direction) by an empty nanochannel from the light scattered by the same channel with a molecule inside. A sequence of differential images of a nanochannel containing a diffusing single molecule obtained in this way is combined into a kymograph in ( D ), which then contains the full molecular trajectory. Here, this is exemplified for a Bovine Serum Albumin (BSA, MW = 66.8 kDa, R s = 3.5 nm) molecule differentially imaged in two nanochannels with different cross sections (defined by the widest and deepest points of the cross sections; see insets for cross-section scanning electron microscope images), i.e., and A I I I = 153nm × 32nm and A I V = 118nm × 30nm. While the trajectory of the BSA molecule is not resolved for the larger A I I I channel when only applying the standard data preprocessing steps outlined in the Methods section, it is clearly visible in the smaller channel A I V . This showcases the potential of lowering the LoD of NSM by reducing the nanochannel cross section area A , since A is inversely proportional to the LoD . For a more detailed statistical analysis of BSA and its dimeric oligomers, we refer to our seminal NSM work . Here, NSM denotes nanofluidic scattering microscopy, BSA bovine serum albumin, MW molecular weight, R s hydrodynamic radius, and LoD limit of detection.
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    Image Search Results


    A Schematic of the nanofluidic chip used. B Zoom-in on the nanofluidic part of the chip depicting the microfluidic inlet and outlet channels that connect to liquid reservoirs used to interface the chip holder and to a set of parallel nanofluidic channels used for NSM experiments. The length of the nanochannels is chosen such that they fit the field of view of the microscope at the desired magnification, and the cross-section of the nanochannels is tailored to the size of the molecule to be analyzed, as discussed in the main text. The two indicated channel dimensions correspond to the two nanochannel types used in the experiment depicted in ( D ). C The principle of differential imaging in NSM, in which we subtract the light scattered (yellow arrows indicate the scattered-light direction) by an empty nanochannel from the light scattered by the same channel with a molecule inside. A sequence of differential images of a nanochannel containing a diffusing single molecule obtained in this way is combined into a kymograph in ( D ), which then contains the full molecular trajectory. Here, this is exemplified for a Bovine Serum Albumin (BSA, MW = 66.8 kDa, R s = 3.5 nm) molecule differentially imaged in two nanochannels with different cross sections (defined by the widest and deepest points of the cross sections; see insets for cross-section scanning electron microscope images), i.e., and A I I I = 153nm × 32nm and A I V = 118nm × 30nm. While the trajectory of the BSA molecule is not resolved for the larger A I I I channel when only applying the standard data preprocessing steps outlined in the Methods section, it is clearly visible in the smaller channel A I V . This showcases the potential of lowering the LoD of NSM by reducing the nanochannel cross section area A , since A is inversely proportional to the LoD . For a more detailed statistical analysis of BSA and its dimeric oligomers, we refer to our seminal NSM work . Here, NSM denotes nanofluidic scattering microscopy, BSA bovine serum albumin, MW molecular weight, R s hydrodynamic radius, and LoD limit of detection.

    Journal: Nature Communications

    Article Title: Label-free mass and size characterization of few-kDa biomolecules by hierarchical vision transformer augmented nanofluidic scattering microscopy

    doi: 10.1038/s41467-026-70514-z

    Figure Lengend Snippet: A Schematic of the nanofluidic chip used. B Zoom-in on the nanofluidic part of the chip depicting the microfluidic inlet and outlet channels that connect to liquid reservoirs used to interface the chip holder and to a set of parallel nanofluidic channels used for NSM experiments. The length of the nanochannels is chosen such that they fit the field of view of the microscope at the desired magnification, and the cross-section of the nanochannels is tailored to the size of the molecule to be analyzed, as discussed in the main text. The two indicated channel dimensions correspond to the two nanochannel types used in the experiment depicted in ( D ). C The principle of differential imaging in NSM, in which we subtract the light scattered (yellow arrows indicate the scattered-light direction) by an empty nanochannel from the light scattered by the same channel with a molecule inside. A sequence of differential images of a nanochannel containing a diffusing single molecule obtained in this way is combined into a kymograph in ( D ), which then contains the full molecular trajectory. Here, this is exemplified for a Bovine Serum Albumin (BSA, MW = 66.8 kDa, R s = 3.5 nm) molecule differentially imaged in two nanochannels with different cross sections (defined by the widest and deepest points of the cross sections; see insets for cross-section scanning electron microscope images), i.e., and A I I I = 153nm × 32nm and A I V = 118nm × 30nm. While the trajectory of the BSA molecule is not resolved for the larger A I I I channel when only applying the standard data preprocessing steps outlined in the Methods section, it is clearly visible in the smaller channel A I V . This showcases the potential of lowering the LoD of NSM by reducing the nanochannel cross section area A , since A is inversely proportional to the LoD . For a more detailed statistical analysis of BSA and its dimeric oligomers, we refer to our seminal NSM work . Here, NSM denotes nanofluidic scattering microscopy, BSA bovine serum albumin, MW molecular weight, R s hydrodynamic radius, and LoD limit of detection.

    Article Snippet: A commercial microscope platform (RM21, Mad City Labs) is used with a micropositioner for sample positioning and a nanopositioner for fine alignment, both by Mad City Labs.

    Techniques: Microscopy, Imaging, Sequencing, Molecular Weight