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86
Inscopix Inc grin lens
Recording and odor presentation paradigm (A) Schematic of the recording apparatus and paradigm. Ten trials of six odorants (BZ = benzaldehyde, C4 = butyraldehyde, E4 = ethyl butyrate, H2 = 2-heptanone, LL = linalool, DP = dimethyl pyrazine) were presented over five consecutive days of passive odor experience while neuronal activity was continuously recorded via miniscope. (B) Example <t>GRIN</t> <t>lens</t> implantation site from one animal in PC; annotated to show the primary layers, scale bar in the bottom left is 250 μm. (C) Example calcium traces from ten neurons recorded over 400 s at the start of a recording session. (D) Mean PID trace (black line, gray bars denote SD) taken from ten presentations of E4 during field presentations. The PID intake port was placed at the back of the chamber opposite the odor port. (E) Individual PID traces from odor pulses as in (D), but with the intake port placed directly in front of the olfactometer output line; black line indicates the first trial and the red line indicates last trial.
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Inscopix Inc gradient index grin lens
Recording and odor presentation paradigm (A) Schematic of the recording apparatus and paradigm. Ten trials of six odorants (BZ = benzaldehyde, C4 = butyraldehyde, E4 = ethyl butyrate, H2 = 2-heptanone, LL = linalool, DP = dimethyl pyrazine) were presented over five consecutive days of passive odor experience while neuronal activity was continuously recorded via miniscope. (B) Example <t>GRIN</t> <t>lens</t> implantation site from one animal in PC; annotated to show the primary layers, scale bar in the bottom left is 250 μm. (C) Example calcium traces from ten neurons recorded over 400 s at the start of a recording session. (D) Mean PID trace (black line, gray bars denote SD) taken from ten presentations of E4 during field presentations. The PID intake port was placed at the back of the chamber opposite the odor port. (E) Individual PID traces from odor pulses as in (D), but with the intake port placed directly in front of the olfactometer output line; black line indicates the first trial and the red line indicates last trial.
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Neuroplex Inc grin lens types
( a ) Surgical paradigm. In a TetO-GCaMP6s × CaMKII-tTa mouse, 9 AAV retro viruses are injected into downstream brain regions and gradient-index <t>(GRIN)</t> <t>lens</t> implanted into the target region. ( b ) Simultaneous recording of GCaMP6s (top) and behavior (bottom) during a social memory task. Scale bar = 100 µm ( c ) GCaMP6s recordings are processed. Constrained non-negative matrix factorization (CNMF)-defined ROIs (top) and ΔF/F traces (bottom) are exported. Scale bar = 100 µm. ( d ) Mice are head fixed and FOV under the GRIN lens imaged using the multiplexed lambda method. ( e ) Transformations are determined using anatomical background images to co-register the two imaging platforms. The transformations are applied to CNMF-defined ROIs. Scale bar = 100 µm. ( f ) Multispectral data are collected for each ROI (top) and an average spectral fingerprint for all ROIs is generated (bottom). Mean ±1.5 SD. Scale bar = 100 µm. ( g ) A linear unmixing model is applied to determine the fluorophore contribution for each ROI. Scale bar = 100 µm. ( i ) Neural activity is sorted by cell type. Scale bars = 20 ΔF/F (vertical), 20 s (horizontal).
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Neuroplex Inc grin lens
( a ) Surgical paradigm. In a TetO-GCaMP6s × CaMKII-tTa mouse, 9 AAV retro viruses are injected into downstream brain regions and gradient-index <t>(GRIN)</t> lens implanted into the target region. ( b ) Simultaneous recording of GCaMP6s (top) and behavior (bottom) during a social memory task. Scale bar = 100 µm ( c ) GCaMP6s recordings are processed. Constrained non-negative matrix factorization (CNMF)-defined ROIs (top) and ΔF/F traces (bottom) are exported. Scale bar = 100 µm. ( d ) Mice are head fixed and FOV under the GRIN lens imaged using the multiplexed lambda method. ( e ) Transformations are determined using anatomical background images to co-register the two imaging platforms. The transformations are applied to CNMF-defined ROIs. Scale bar = 100 µm. ( f ) Multispectral data are collected for each ROI (top) and an average spectral fingerprint for all ROIs is generated (bottom). Mean ±1.5 SD. Scale bar = 100 µm. ( g ) A linear unmixing model is applied to determine <t>the</t> <t>fluorophore</t> contribution for each ROI. Scale bar = 100 µm. ( i ) Neural activity is sorted by cell type. Scale bars = 20 ΔF/F (vertical), 20 s (horizontal).
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Neuroplex Inc head mounted grin lens based miniscope imaging
Video showing animal behavior during the social memory task alongside the corresponding miniscope calcium recording from the same session. Calcium-active ROIs are pseudocolored according to their Neuroplex-assigned fluorophore identity, indicating the corresponding projection-defined neuronal population.
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86
Neuroplex Inc grin lens in vivo
( a ) Surgical paradigm. In a TetO-GCaMP6s × CaMKII-tTa mouse, 9 AAV retro viruses are injected into downstream brain regions and gradient-index <t>(GRIN)</t> <t>lens</t> <t>implanted</t> into the target region. ( b ) Simultaneous recording of GCaMP6s (top) and behavior (bottom) during a social memory task. Scale bar = 100 µm ( c ) GCaMP6s recordings are processed. Constrained non-negative matrix factorization (CNMF)-defined ROIs (top) and ΔF/F traces (bottom) are exported. Scale bar = 100 µm. ( d ) Mice are head fixed and FOV under the GRIN lens imaged using the multiplexed lambda method. ( e ) Transformations are determined using anatomical background images to co-register the two imaging platforms. The transformations are applied to CNMF-defined ROIs. Scale bar = 100 µm. ( f ) Multispectral data are collected for each ROI (top) and an average spectral fingerprint for all ROIs is generated (bottom). Mean ±1.5 SD. Scale bar = 100 µm. ( g ) A linear unmixing model is applied to determine the fluorophore contribution for each ROI. Scale bar = 100 µm. ( i ) Neural activity is sorted by cell type. Scale bars = 20 ΔF/F (vertical), 20 s (horizontal).
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Image Search Results


Recording and odor presentation paradigm (A) Schematic of the recording apparatus and paradigm. Ten trials of six odorants (BZ = benzaldehyde, C4 = butyraldehyde, E4 = ethyl butyrate, H2 = 2-heptanone, LL = linalool, DP = dimethyl pyrazine) were presented over five consecutive days of passive odor experience while neuronal activity was continuously recorded via miniscope. (B) Example GRIN lens implantation site from one animal in PC; annotated to show the primary layers, scale bar in the bottom left is 250 μm. (C) Example calcium traces from ten neurons recorded over 400 s at the start of a recording session. (D) Mean PID trace (black line, gray bars denote SD) taken from ten presentations of E4 during field presentations. The PID intake port was placed at the back of the chamber opposite the odor port. (E) Individual PID traces from odor pulses as in (D), but with the intake port placed directly in front of the olfactometer output line; black line indicates the first trial and the red line indicates last trial.

Journal: iScience

Article Title: Experience and behavior modulate piriform cortex odor representation in freely moving mice

doi: 10.1016/j.isci.2026.115897

Figure Lengend Snippet: Recording and odor presentation paradigm (A) Schematic of the recording apparatus and paradigm. Ten trials of six odorants (BZ = benzaldehyde, C4 = butyraldehyde, E4 = ethyl butyrate, H2 = 2-heptanone, LL = linalool, DP = dimethyl pyrazine) were presented over five consecutive days of passive odor experience while neuronal activity was continuously recorded via miniscope. (B) Example GRIN lens implantation site from one animal in PC; annotated to show the primary layers, scale bar in the bottom left is 250 μm. (C) Example calcium traces from ten neurons recorded over 400 s at the start of a recording session. (D) Mean PID trace (black line, gray bars denote SD) taken from ten presentations of E4 during field presentations. The PID intake port was placed at the back of the chamber opposite the odor port. (E) Individual PID traces from odor pulses as in (D), but with the intake port placed directly in front of the olfactometer output line; black line indicates the first trial and the red line indicates last trial.

Article Snippet: GRIN lens , Inscopix , 0.5 × 6.1 mm lens.

Techniques: Activity Assay

( a ) Surgical paradigm. In a TetO-GCaMP6s × CaMKII-tTa mouse, 9 AAV retro viruses are injected into downstream brain regions and gradient-index (GRIN) lens implanted into the target region. ( b ) Simultaneous recording of GCaMP6s (top) and behavior (bottom) during a social memory task. Scale bar = 100 µm ( c ) GCaMP6s recordings are processed. Constrained non-negative matrix factorization (CNMF)-defined ROIs (top) and ΔF/F traces (bottom) are exported. Scale bar = 100 µm. ( d ) Mice are head fixed and FOV under the GRIN lens imaged using the multiplexed lambda method. ( e ) Transformations are determined using anatomical background images to co-register the two imaging platforms. The transformations are applied to CNMF-defined ROIs. Scale bar = 100 µm. ( f ) Multispectral data are collected for each ROI (top) and an average spectral fingerprint for all ROIs is generated (bottom). Mean ±1.5 SD. Scale bar = 100 µm. ( g ) A linear unmixing model is applied to determine the fluorophore contribution for each ROI. Scale bar = 100 µm. ( i ) Neural activity is sorted by cell type. Scale bars = 20 ΔF/F (vertical), 20 s (horizontal).

Journal: eLife

Article Title: Functional imaging of nine distinct neuronal populations under a miniscope in freely behaving animals

doi: 10.7554/eLife.110277

Figure Lengend Snippet: ( a ) Surgical paradigm. In a TetO-GCaMP6s × CaMKII-tTa mouse, 9 AAV retro viruses are injected into downstream brain regions and gradient-index (GRIN) lens implanted into the target region. ( b ) Simultaneous recording of GCaMP6s (top) and behavior (bottom) during a social memory task. Scale bar = 100 µm ( c ) GCaMP6s recordings are processed. Constrained non-negative matrix factorization (CNMF)-defined ROIs (top) and ΔF/F traces (bottom) are exported. Scale bar = 100 µm. ( d ) Mice are head fixed and FOV under the GRIN lens imaged using the multiplexed lambda method. ( e ) Transformations are determined using anatomical background images to co-register the two imaging platforms. The transformations are applied to CNMF-defined ROIs. Scale bar = 100 µm. ( f ) Multispectral data are collected for each ROI (top) and an average spectral fingerprint for all ROIs is generated (bottom). Mean ±1.5 SD. Scale bar = 100 µm. ( g ) A linear unmixing model is applied to determine the fluorophore contribution for each ROI. Scale bar = 100 µm. ( i ) Neural activity is sorted by cell type. Scale bars = 20 ΔF/F (vertical), 20 s (horizontal).

Article Snippet: Neuroplex is compatible with a variety of GRIN lens types and sizes, as well as with cranial windows.

Techniques: Injection, Imaging, Generated, Activity Assay

( a ) Multicolor image obtained through 1×4 mm silver-doped GRIN lens of the calibration slide highlighting the z-plane chromatic aberration. ( b ) Shift in z-focal plane as a function of excitation laser wavelength. Second-order polynomial R 2 =0.9926, n=5. ( c ) Orthogonal projection of multicolor image obtained through 1×4 mm silver-doped GRIN lens of the calibration slide. Intensity profile (below) of single ring for each excitation channel shows negligible chromatic shift along lateral axes. ( d ) Percent transmission through the GRIN lens as a function of excitation laser wavelength. Sixth order polynomial R 2 =0.9751, n=5. ( e ) Orthogonal projection of calibration slide imaged through 1×4 mm silver-doped GRIN lens overlaid (in cyan) with rectilinear grid lines. Substantial overlap of fluorescent rings from the grid indicates minimal field distortions. ( f ) Excerpt from ( e ) showing the rings focused in the sagittal plane (z=+20 µm), the circle of least confusion (z=0 µm), and the tangential focal plane (z=–17.5 µm). ( g ) Curvature of the Petzval field as a function of radial distance from center of the GRIN lens. Astigmatism results in three axially separated focal planes. Second order polynomial sagittal R 2 =0.9845, least confusion R 2 =0.8839, and tangential R 2 =0.7519, n=3. Scale bars = 100 µm.

Journal: eLife

Article Title: Functional imaging of nine distinct neuronal populations under a miniscope in freely behaving animals

doi: 10.7554/eLife.110277

Figure Lengend Snippet: ( a ) Multicolor image obtained through 1×4 mm silver-doped GRIN lens of the calibration slide highlighting the z-plane chromatic aberration. ( b ) Shift in z-focal plane as a function of excitation laser wavelength. Second-order polynomial R 2 =0.9926, n=5. ( c ) Orthogonal projection of multicolor image obtained through 1×4 mm silver-doped GRIN lens of the calibration slide. Intensity profile (below) of single ring for each excitation channel shows negligible chromatic shift along lateral axes. ( d ) Percent transmission through the GRIN lens as a function of excitation laser wavelength. Sixth order polynomial R 2 =0.9751, n=5. ( e ) Orthogonal projection of calibration slide imaged through 1×4 mm silver-doped GRIN lens overlaid (in cyan) with rectilinear grid lines. Substantial overlap of fluorescent rings from the grid indicates minimal field distortions. ( f ) Excerpt from ( e ) showing the rings focused in the sagittal plane (z=+20 µm), the circle of least confusion (z=0 µm), and the tangential focal plane (z=–17.5 µm). ( g ) Curvature of the Petzval field as a function of radial distance from center of the GRIN lens. Astigmatism results in three axially separated focal planes. Second order polynomial sagittal R 2 =0.9845, least confusion R 2 =0.8839, and tangential R 2 =0.7519, n=3. Scale bars = 100 µm.

Article Snippet: Neuroplex is compatible with a variety of GRIN lens types and sizes, as well as with cranial windows.

Techniques: Transmission Assay

( a ) Shift in z-focal plane as a function of excitation laser wavelength in a 1×4 mm silver-doped GRIN lens. Second-order polynomial R 2 =0.9970. ( b ) Shift in z-focal plane as a function of excitation laser wavelength in 0.6×7 mm GRIN lenses doped with either silver or lithium. Second-order polynomials: Silver R 2 =0.9983, Lithium R 2 =0.9928. ( c ) Percent transmission through a 1×4 mm silver-doped GRIN lens as a function of excitation laser wavelength. Sixth-order polynomial R 2 =0.9926. ( d ) Percent transmission through 0.6×7 mm GRIN lenses doped with either silver or lithium as a function of excitation laser wavelength. Sixth-order polynomial: silver, R 2 =0.9979; lithium, R 2 =0.9549.

Journal: eLife

Article Title: Functional imaging of nine distinct neuronal populations under a miniscope in freely behaving animals

doi: 10.7554/eLife.110277

Figure Lengend Snippet: ( a ) Shift in z-focal plane as a function of excitation laser wavelength in a 1×4 mm silver-doped GRIN lens. Second-order polynomial R 2 =0.9970. ( b ) Shift in z-focal plane as a function of excitation laser wavelength in 0.6×7 mm GRIN lenses doped with either silver or lithium. Second-order polynomials: Silver R 2 =0.9983, Lithium R 2 =0.9928. ( c ) Percent transmission through a 1×4 mm silver-doped GRIN lens as a function of excitation laser wavelength. Sixth-order polynomial R 2 =0.9926. ( d ) Percent transmission through 0.6×7 mm GRIN lenses doped with either silver or lithium as a function of excitation laser wavelength. Sixth-order polynomial: silver, R 2 =0.9979; lithium, R 2 =0.9549.

Article Snippet: Neuroplex is compatible with a variety of GRIN lens types and sizes, as well as with cranial windows.

Techniques: Transmission Assay

( a ) Surgical paradigm. In a TetO-GCaMP6s × CaMKII-tTa mouse, 9 AAV retro viruses are injected into downstream brain regions and gradient-index (GRIN) lens implanted into the target region. ( b ) Simultaneous recording of GCaMP6s (top) and behavior (bottom) during a social memory task. Scale bar = 100 µm ( c ) GCaMP6s recordings are processed. Constrained non-negative matrix factorization (CNMF)-defined ROIs (top) and ΔF/F traces (bottom) are exported. Scale bar = 100 µm. ( d ) Mice are head fixed and FOV under the GRIN lens imaged using the multiplexed lambda method. ( e ) Transformations are determined using anatomical background images to co-register the two imaging platforms. The transformations are applied to CNMF-defined ROIs. Scale bar = 100 µm. ( f ) Multispectral data are collected for each ROI (top) and an average spectral fingerprint for all ROIs is generated (bottom). Mean ±1.5 SD. Scale bar = 100 µm. ( g ) A linear unmixing model is applied to determine the fluorophore contribution for each ROI. Scale bar = 100 µm. ( i ) Neural activity is sorted by cell type. Scale bars = 20 ΔF/F (vertical), 20 s (horizontal).

Journal: eLife

Article Title: Functional imaging of nine distinct neuronal populations under a miniscope in freely behaving animals

doi: 10.7554/eLife.110277

Figure Lengend Snippet: ( a ) Surgical paradigm. In a TetO-GCaMP6s × CaMKII-tTa mouse, 9 AAV retro viruses are injected into downstream brain regions and gradient-index (GRIN) lens implanted into the target region. ( b ) Simultaneous recording of GCaMP6s (top) and behavior (bottom) during a social memory task. Scale bar = 100 µm ( c ) GCaMP6s recordings are processed. Constrained non-negative matrix factorization (CNMF)-defined ROIs (top) and ΔF/F traces (bottom) are exported. Scale bar = 100 µm. ( d ) Mice are head fixed and FOV under the GRIN lens imaged using the multiplexed lambda method. ( e ) Transformations are determined using anatomical background images to co-register the two imaging platforms. The transformations are applied to CNMF-defined ROIs. Scale bar = 100 µm. ( f ) Multispectral data are collected for each ROI (top) and an average spectral fingerprint for all ROIs is generated (bottom). Mean ±1.5 SD. Scale bar = 100 µm. ( g ) A linear unmixing model is applied to determine the fluorophore contribution for each ROI. Scale bar = 100 µm. ( i ) Neural activity is sorted by cell type. Scale bars = 20 ΔF/F (vertical), 20 s (horizontal).

Article Snippet: We demonstrate that Neuroplex allows for the identification of up to nine fluorophore-labeled neuronal subtypes during in vivo calcium imaging through a GRIN lens ( ).

Techniques: Injection, Imaging, Generated, Activity Assay

( a ) Multicolor image obtained through 1×4 mm silver-doped GRIN lens of the calibration slide highlighting the z-plane chromatic aberration. ( b ) Shift in z-focal plane as a function of excitation laser wavelength. Second-order polynomial R 2 =0.9926, n=5. ( c ) Orthogonal projection of multicolor image obtained through 1×4 mm silver-doped GRIN lens of the calibration slide. Intensity profile (below) of single ring for each excitation channel shows negligible chromatic shift along lateral axes. ( d ) Percent transmission through the GRIN lens as a function of excitation laser wavelength. Sixth order polynomial R 2 =0.9751, n=5. ( e ) Orthogonal projection of calibration slide imaged through 1×4 mm silver-doped GRIN lens overlaid (in cyan) with rectilinear grid lines. Substantial overlap of fluorescent rings from the grid indicates minimal field distortions. ( f ) Excerpt from ( e ) showing the rings focused in the sagittal plane (z=+20 µm), the circle of least confusion (z=0 µm), and the tangential focal plane (z=–17.5 µm). ( g ) Curvature of the Petzval field as a function of radial distance from center of the GRIN lens. Astigmatism results in three axially separated focal planes. Second order polynomial sagittal R 2 =0.9845, least confusion R 2 =0.8839, and tangential R 2 =0.7519, n=3. Scale bars = 100 µm.

Journal: eLife

Article Title: Functional imaging of nine distinct neuronal populations under a miniscope in freely behaving animals

doi: 10.7554/eLife.110277

Figure Lengend Snippet: ( a ) Multicolor image obtained through 1×4 mm silver-doped GRIN lens of the calibration slide highlighting the z-plane chromatic aberration. ( b ) Shift in z-focal plane as a function of excitation laser wavelength. Second-order polynomial R 2 =0.9926, n=5. ( c ) Orthogonal projection of multicolor image obtained through 1×4 mm silver-doped GRIN lens of the calibration slide. Intensity profile (below) of single ring for each excitation channel shows negligible chromatic shift along lateral axes. ( d ) Percent transmission through the GRIN lens as a function of excitation laser wavelength. Sixth order polynomial R 2 =0.9751, n=5. ( e ) Orthogonal projection of calibration slide imaged through 1×4 mm silver-doped GRIN lens overlaid (in cyan) with rectilinear grid lines. Substantial overlap of fluorescent rings from the grid indicates minimal field distortions. ( f ) Excerpt from ( e ) showing the rings focused in the sagittal plane (z=+20 µm), the circle of least confusion (z=0 µm), and the tangential focal plane (z=–17.5 µm). ( g ) Curvature of the Petzval field as a function of radial distance from center of the GRIN lens. Astigmatism results in three axially separated focal planes. Second order polynomial sagittal R 2 =0.9845, least confusion R 2 =0.8839, and tangential R 2 =0.7519, n=3. Scale bars = 100 µm.

Article Snippet: We demonstrate that Neuroplex allows for the identification of up to nine fluorophore-labeled neuronal subtypes during in vivo calcium imaging through a GRIN lens ( ).

Techniques: Transmission Assay

( a ) Shift in z-focal plane as a function of excitation laser wavelength in a 1×4 mm silver-doped GRIN lens. Second-order polynomial R 2 =0.9970. ( b ) Shift in z-focal plane as a function of excitation laser wavelength in 0.6×7 mm GRIN lenses doped with either silver or lithium. Second-order polynomials: Silver R 2 =0.9983, Lithium R 2 =0.9928. ( c ) Percent transmission through a 1×4 mm silver-doped GRIN lens as a function of excitation laser wavelength. Sixth-order polynomial R 2 =0.9926. ( d ) Percent transmission through 0.6×7 mm GRIN lenses doped with either silver or lithium as a function of excitation laser wavelength. Sixth-order polynomial: silver, R 2 =0.9979; lithium, R 2 =0.9549.

Journal: eLife

Article Title: Functional imaging of nine distinct neuronal populations under a miniscope in freely behaving animals

doi: 10.7554/eLife.110277

Figure Lengend Snippet: ( a ) Shift in z-focal plane as a function of excitation laser wavelength in a 1×4 mm silver-doped GRIN lens. Second-order polynomial R 2 =0.9970. ( b ) Shift in z-focal plane as a function of excitation laser wavelength in 0.6×7 mm GRIN lenses doped with either silver or lithium. Second-order polynomials: Silver R 2 =0.9983, Lithium R 2 =0.9928. ( c ) Percent transmission through a 1×4 mm silver-doped GRIN lens as a function of excitation laser wavelength. Sixth-order polynomial R 2 =0.9926. ( d ) Percent transmission through 0.6×7 mm GRIN lenses doped with either silver or lithium as a function of excitation laser wavelength. Sixth-order polynomial: silver, R 2 =0.9979; lithium, R 2 =0.9549.

Article Snippet: We demonstrate that Neuroplex allows for the identification of up to nine fluorophore-labeled neuronal subtypes during in vivo calcium imaging through a GRIN lens ( ).

Techniques: Transmission Assay

Video showing animal behavior during the social memory task alongside the corresponding miniscope calcium recording from the same session. Calcium-active ROIs are pseudocolored according to their Neuroplex-assigned fluorophore identity, indicating the corresponding projection-defined neuronal population.

Journal: eLife

Article Title: Functional imaging of nine distinct neuronal populations under a miniscope in freely behaving animals

doi: 10.7554/eLife.110277

Figure Lengend Snippet: Video showing animal behavior during the social memory task alongside the corresponding miniscope calcium recording from the same session. Calcium-active ROIs are pseudocolored according to their Neuroplex-assigned fluorophore identity, indicating the corresponding projection-defined neuronal population.

Article Snippet: Neuroplex enables simultaneous tracking of multiple neuronal subtypes in behaving animals through a three-step pipeline: (1) Head-mounted GRIN-lens based miniscope imaging of GCaMP activity during behavior; (2) in vivo multiplexed confocal spectral imaging through the same GRIN lens to capture fluorophore fingerprints; and (3) linear unmixing to assign projection-specific identities to functionally defined neurons ( ).

Techniques:

( a ) Surgical paradigm. In a TetO-GCaMP6s × CaMKII-tTa mouse, 9 AAV retro viruses are injected into downstream brain regions and gradient-index (GRIN) lens implanted into the target region. ( b ) Simultaneous recording of GCaMP6s (top) and behavior (bottom) during a social memory task. Scale bar = 100 µm ( c ) GCaMP6s recordings are processed. Constrained non-negative matrix factorization (CNMF)-defined ROIs (top) and ΔF/F traces (bottom) are exported. Scale bar = 100 µm. ( d ) Mice are head fixed and FOV under the GRIN lens imaged using the multiplexed lambda method. ( e ) Transformations are determined using anatomical background images to co-register the two imaging platforms. The transformations are applied to CNMF-defined ROIs. Scale bar = 100 µm. ( f ) Multispectral data are collected for each ROI (top) and an average spectral fingerprint for all ROIs is generated (bottom). Mean ±1.5 SD. Scale bar = 100 µm. ( g ) A linear unmixing model is applied to determine the fluorophore contribution for each ROI. Scale bar = 100 µm. ( i ) Neural activity is sorted by cell type. Scale bars = 20 ΔF/F (vertical), 20 s (horizontal).

Journal: eLife

Article Title: Functional imaging of nine distinct neuronal populations under a miniscope in freely behaving animals

doi: 10.7554/eLife.110277

Figure Lengend Snippet: ( a ) Surgical paradigm. In a TetO-GCaMP6s × CaMKII-tTa mouse, 9 AAV retro viruses are injected into downstream brain regions and gradient-index (GRIN) lens implanted into the target region. ( b ) Simultaneous recording of GCaMP6s (top) and behavior (bottom) during a social memory task. Scale bar = 100 µm ( c ) GCaMP6s recordings are processed. Constrained non-negative matrix factorization (CNMF)-defined ROIs (top) and ΔF/F traces (bottom) are exported. Scale bar = 100 µm. ( d ) Mice are head fixed and FOV under the GRIN lens imaged using the multiplexed lambda method. ( e ) Transformations are determined using anatomical background images to co-register the two imaging platforms. The transformations are applied to CNMF-defined ROIs. Scale bar = 100 µm. ( f ) Multispectral data are collected for each ROI (top) and an average spectral fingerprint for all ROIs is generated (bottom). Mean ±1.5 SD. Scale bar = 100 µm. ( g ) A linear unmixing model is applied to determine the fluorophore contribution for each ROI. Scale bar = 100 µm. ( i ) Neural activity is sorted by cell type. Scale bars = 20 ΔF/F (vertical), 20 s (horizontal).

Article Snippet: Neuroplex enables simultaneous tracking of multiple neuronal subtypes in behaving animals through a three-step pipeline: (1) Head-mounted GRIN-lens based miniscope imaging of GCaMP activity during behavior; (2) in vivo multiplexed confocal spectral imaging through the same GRIN lens to capture fluorophore fingerprints; and (3) linear unmixing to assign projection-specific identities to functionally defined neurons ( ).

Techniques: Injection, Imaging, Generated, Activity Assay

( a ) Multicolor image obtained through 1×4 mm silver-doped GRIN lens of the calibration slide highlighting the z-plane chromatic aberration. ( b ) Shift in z-focal plane as a function of excitation laser wavelength. Second-order polynomial R 2 =0.9926, n=5. ( c ) Orthogonal projection of multicolor image obtained through 1×4 mm silver-doped GRIN lens of the calibration slide. Intensity profile (below) of single ring for each excitation channel shows negligible chromatic shift along lateral axes. ( d ) Percent transmission through the GRIN lens as a function of excitation laser wavelength. Sixth order polynomial R 2 =0.9751, n=5. ( e ) Orthogonal projection of calibration slide imaged through 1×4 mm silver-doped GRIN lens overlaid (in cyan) with rectilinear grid lines. Substantial overlap of fluorescent rings from the grid indicates minimal field distortions. ( f ) Excerpt from ( e ) showing the rings focused in the sagittal plane (z=+20 µm), the circle of least confusion (z=0 µm), and the tangential focal plane (z=–17.5 µm). ( g ) Curvature of the Petzval field as a function of radial distance from center of the GRIN lens. Astigmatism results in three axially separated focal planes. Second order polynomial sagittal R 2 =0.9845, least confusion R 2 =0.8839, and tangential R 2 =0.7519, n=3. Scale bars = 100 µm.

Journal: eLife

Article Title: Functional imaging of nine distinct neuronal populations under a miniscope in freely behaving animals

doi: 10.7554/eLife.110277

Figure Lengend Snippet: ( a ) Multicolor image obtained through 1×4 mm silver-doped GRIN lens of the calibration slide highlighting the z-plane chromatic aberration. ( b ) Shift in z-focal plane as a function of excitation laser wavelength. Second-order polynomial R 2 =0.9926, n=5. ( c ) Orthogonal projection of multicolor image obtained through 1×4 mm silver-doped GRIN lens of the calibration slide. Intensity profile (below) of single ring for each excitation channel shows negligible chromatic shift along lateral axes. ( d ) Percent transmission through the GRIN lens as a function of excitation laser wavelength. Sixth order polynomial R 2 =0.9751, n=5. ( e ) Orthogonal projection of calibration slide imaged through 1×4 mm silver-doped GRIN lens overlaid (in cyan) with rectilinear grid lines. Substantial overlap of fluorescent rings from the grid indicates minimal field distortions. ( f ) Excerpt from ( e ) showing the rings focused in the sagittal plane (z=+20 µm), the circle of least confusion (z=0 µm), and the tangential focal plane (z=–17.5 µm). ( g ) Curvature of the Petzval field as a function of radial distance from center of the GRIN lens. Astigmatism results in three axially separated focal planes. Second order polynomial sagittal R 2 =0.9845, least confusion R 2 =0.8839, and tangential R 2 =0.7519, n=3. Scale bars = 100 µm.

Article Snippet: Neuroplex enables simultaneous tracking of multiple neuronal subtypes in behaving animals through a three-step pipeline: (1) Head-mounted GRIN-lens based miniscope imaging of GCaMP activity during behavior; (2) in vivo multiplexed confocal spectral imaging through the same GRIN lens to capture fluorophore fingerprints; and (3) linear unmixing to assign projection-specific identities to functionally defined neurons ( ).

Techniques: Transmission Assay

( a ) Shift in z-focal plane as a function of excitation laser wavelength in a 1×4 mm silver-doped GRIN lens. Second-order polynomial R 2 =0.9970. ( b ) Shift in z-focal plane as a function of excitation laser wavelength in 0.6×7 mm GRIN lenses doped with either silver or lithium. Second-order polynomials: Silver R 2 =0.9983, Lithium R 2 =0.9928. ( c ) Percent transmission through a 1×4 mm silver-doped GRIN lens as a function of excitation laser wavelength. Sixth-order polynomial R 2 =0.9926. ( d ) Percent transmission through 0.6×7 mm GRIN lenses doped with either silver or lithium as a function of excitation laser wavelength. Sixth-order polynomial: silver, R 2 =0.9979; lithium, R 2 =0.9549.

Journal: eLife

Article Title: Functional imaging of nine distinct neuronal populations under a miniscope in freely behaving animals

doi: 10.7554/eLife.110277

Figure Lengend Snippet: ( a ) Shift in z-focal plane as a function of excitation laser wavelength in a 1×4 mm silver-doped GRIN lens. Second-order polynomial R 2 =0.9970. ( b ) Shift in z-focal plane as a function of excitation laser wavelength in 0.6×7 mm GRIN lenses doped with either silver or lithium. Second-order polynomials: Silver R 2 =0.9983, Lithium R 2 =0.9928. ( c ) Percent transmission through a 1×4 mm silver-doped GRIN lens as a function of excitation laser wavelength. Sixth-order polynomial R 2 =0.9926. ( d ) Percent transmission through 0.6×7 mm GRIN lenses doped with either silver or lithium as a function of excitation laser wavelength. Sixth-order polynomial: silver, R 2 =0.9979; lithium, R 2 =0.9549.

Article Snippet: Neuroplex enables simultaneous tracking of multiple neuronal subtypes in behaving animals through a three-step pipeline: (1) Head-mounted GRIN-lens based miniscope imaging of GCaMP activity during behavior; (2) in vivo multiplexed confocal spectral imaging through the same GRIN lens to capture fluorophore fingerprints; and (3) linear unmixing to assign projection-specific identities to functionally defined neurons ( ).

Techniques: Transmission Assay

( a ) In vivo multiplexed spectral imaging paradigm. Schematic of multiplexed spectral imaging (left). Depiction of overlapping fluorophore spectral emissions for each excitation laser wavelength (middle). Depiction of multiplexed spectral images which create a 204-dimensional dataset (right). ( b ) Automated co-registration of miniscope and laser scanning confocal microscope (LSM) images. Top: A calibration slide used to measure scaling between modalities. Bottom: Experimental FOV showing brain vasculature. Miniscope and confocal images of the same FOV and automated co-registration overlay with zoomed-in regions of interest. ( c ) Example calcium-activity regions of interest (ROI) derived from miniscope data co-registered and overlaid on confocal LSM image. ( d ) Spectral fingerprint of the example ROI, with the solid blue line showing the example ROI and the dashed line depicting the average spectral profile of the animal. ( e ) Beta multiplier from the example ROI, depicting the deviation from the mean beta value for all ROIs from the same animal. ( f ) Empirically measured spectral profiles from pure fluorophore samples, shown as beta-weighted contributors to ROI fingerprints. Scale bar: 100 µm ( a, b ), 10 µm ( b inset and c ).

Journal: eLife

Article Title: Functional imaging of nine distinct neuronal populations under a miniscope in freely behaving animals

doi: 10.7554/eLife.110277

Figure Lengend Snippet: ( a ) In vivo multiplexed spectral imaging paradigm. Schematic of multiplexed spectral imaging (left). Depiction of overlapping fluorophore spectral emissions for each excitation laser wavelength (middle). Depiction of multiplexed spectral images which create a 204-dimensional dataset (right). ( b ) Automated co-registration of miniscope and laser scanning confocal microscope (LSM) images. Top: A calibration slide used to measure scaling between modalities. Bottom: Experimental FOV showing brain vasculature. Miniscope and confocal images of the same FOV and automated co-registration overlay with zoomed-in regions of interest. ( c ) Example calcium-activity regions of interest (ROI) derived from miniscope data co-registered and overlaid on confocal LSM image. ( d ) Spectral fingerprint of the example ROI, with the solid blue line showing the example ROI and the dashed line depicting the average spectral profile of the animal. ( e ) Beta multiplier from the example ROI, depicting the deviation from the mean beta value for all ROIs from the same animal. ( f ) Empirically measured spectral profiles from pure fluorophore samples, shown as beta-weighted contributors to ROI fingerprints. Scale bar: 100 µm ( a, b ), 10 µm ( b inset and c ).

Article Snippet: Neuroplex enables simultaneous tracking of multiple neuronal subtypes in behaving animals through a three-step pipeline: (1) Head-mounted GRIN-lens based miniscope imaging of GCaMP activity during behavior; (2) in vivo multiplexed confocal spectral imaging through the same GRIN lens to capture fluorophore fingerprints; and (3) linear unmixing to assign projection-specific identities to functionally defined neurons ( ).

Techniques: In Vivo, Imaging, Microscopy, Activity Assay, Derivative Assay

( a–r ) Each panel shows an regions of interest (ROI) that exceeded threshold for a single fluorophore identity assignment. (Left:) Functional ROIs identified from miniscope recordings during behavior, co-registered and overlaid on corresponding in vivo confocal images. (Center:) Spectral fingerprint of the ROI (solid line), compared to the animal’s average spectral background (dashed line). Excitation-emission bins are color-coded to excitation laser wavelength. Right inset: Beta multiplier values for all fluorophores from the same ROI, plotted as standard deviations above the animal-specific baseline. Scale bars = 10 µm.

Journal: eLife

Article Title: Functional imaging of nine distinct neuronal populations under a miniscope in freely behaving animals

doi: 10.7554/eLife.110277

Figure Lengend Snippet: ( a–r ) Each panel shows an regions of interest (ROI) that exceeded threshold for a single fluorophore identity assignment. (Left:) Functional ROIs identified from miniscope recordings during behavior, co-registered and overlaid on corresponding in vivo confocal images. (Center:) Spectral fingerprint of the ROI (solid line), compared to the animal’s average spectral background (dashed line). Excitation-emission bins are color-coded to excitation laser wavelength. Right inset: Beta multiplier values for all fluorophores from the same ROI, plotted as standard deviations above the animal-specific baseline. Scale bars = 10 µm.

Article Snippet: Neuroplex enables simultaneous tracking of multiple neuronal subtypes in behaving animals through a three-step pipeline: (1) Head-mounted GRIN-lens based miniscope imaging of GCaMP activity during behavior; (2) in vivo multiplexed confocal spectral imaging through the same GRIN lens to capture fluorophore fingerprints; and (3) linear unmixing to assign projection-specific identities to functionally defined neurons ( ).

Techniques: Functional Assay, In Vivo

( a ) Proportion of functionally defined ROIs classified as expressing one or two fluorophores based on thresholded beta multipliers. ( b ) Frequency of dual fluorophore assignments across the dataset. Left: Heatmap showing co-assignment rates between fluorophore pairs. Right: Total frequency of dual hits per individual fluorophore. ( c ) Frequency of dual-labeled ROIs by brain region. Left: Heatmap showing co-occurrence between projection-defined populations. Right: Total frequency of dual hits per primary brain region. (n=1327 ROIs) ( d ) Example ROIs from miniscope imaging co-registered with confocal lambda stacks. ROIs are overlaid on three excitation channels (405, 561, 639 nm). ( e ) Z-scored beta multipliers across all fluorophores for each example ROI, with above-threshold values circled. Dual fluorophores were assigned to two ROIs (28, 98), and only a single fluorophore to ROI 142. ( f ) Spectral fingerprints for each example ROI (solid line) plotted against the average background spectrum for the animal (dashed line). ROI 28 (top) was assigned two spectrally distinct fluorophores (mTagBFP2+mNeptune2.5); ROI 98 (middle) shows co-assignment of more spectrally overlapping fluorophores (mOrange2+mNeptune2.5); ROI 142 (bottom) is included as a single-label example with a strong match to mTagBFP2 only. Scale bars = 10 µm.

Journal: eLife

Article Title: Functional imaging of nine distinct neuronal populations under a miniscope in freely behaving animals

doi: 10.7554/eLife.110277

Figure Lengend Snippet: ( a ) Proportion of functionally defined ROIs classified as expressing one or two fluorophores based on thresholded beta multipliers. ( b ) Frequency of dual fluorophore assignments across the dataset. Left: Heatmap showing co-assignment rates between fluorophore pairs. Right: Total frequency of dual hits per individual fluorophore. ( c ) Frequency of dual-labeled ROIs by brain region. Left: Heatmap showing co-occurrence between projection-defined populations. Right: Total frequency of dual hits per primary brain region. (n=1327 ROIs) ( d ) Example ROIs from miniscope imaging co-registered with confocal lambda stacks. ROIs are overlaid on three excitation channels (405, 561, 639 nm). ( e ) Z-scored beta multipliers across all fluorophores for each example ROI, with above-threshold values circled. Dual fluorophores were assigned to two ROIs (28, 98), and only a single fluorophore to ROI 142. ( f ) Spectral fingerprints for each example ROI (solid line) plotted against the average background spectrum for the animal (dashed line). ROI 28 (top) was assigned two spectrally distinct fluorophores (mTagBFP2+mNeptune2.5); ROI 98 (middle) shows co-assignment of more spectrally overlapping fluorophores (mOrange2+mNeptune2.5); ROI 142 (bottom) is included as a single-label example with a strong match to mTagBFP2 only. Scale bars = 10 µm.

Article Snippet: Neuroplex enables simultaneous tracking of multiple neuronal subtypes in behaving animals through a three-step pipeline: (1) Head-mounted GRIN-lens based miniscope imaging of GCaMP activity during behavior; (2) in vivo multiplexed confocal spectral imaging through the same GRIN lens to capture fluorophore fingerprints; and (3) linear unmixing to assign projection-specific identities to functionally defined neurons ( ).

Techniques: Expressing, Labeling, Imaging

( a ) Surgical paradigm. In a TetO-GCaMP6s × CaMKII-tTa mouse, 9 AAV retro viruses are injected into downstream brain regions and gradient-index (GRIN) lens implanted into the target region. ( b ) Simultaneous recording of GCaMP6s (top) and behavior (bottom) during a social memory task. Scale bar = 100 µm ( c ) GCaMP6s recordings are processed. Constrained non-negative matrix factorization (CNMF)-defined ROIs (top) and ΔF/F traces (bottom) are exported. Scale bar = 100 µm. ( d ) Mice are head fixed and FOV under the GRIN lens imaged using the multiplexed lambda method. ( e ) Transformations are determined using anatomical background images to co-register the two imaging platforms. The transformations are applied to CNMF-defined ROIs. Scale bar = 100 µm. ( f ) Multispectral data are collected for each ROI (top) and an average spectral fingerprint for all ROIs is generated (bottom). Mean ±1.5 SD. Scale bar = 100 µm. ( g ) A linear unmixing model is applied to determine the fluorophore contribution for each ROI. Scale bar = 100 µm. ( i ) Neural activity is sorted by cell type. Scale bars = 20 ΔF/F (vertical), 20 s (horizontal).

Journal: eLife

Article Title: Functional imaging of nine distinct neuronal populations under a miniscope in freely behaving animals

doi: 10.7554/eLife.110277

Figure Lengend Snippet: ( a ) Surgical paradigm. In a TetO-GCaMP6s × CaMKII-tTa mouse, 9 AAV retro viruses are injected into downstream brain regions and gradient-index (GRIN) lens implanted into the target region. ( b ) Simultaneous recording of GCaMP6s (top) and behavior (bottom) during a social memory task. Scale bar = 100 µm ( c ) GCaMP6s recordings are processed. Constrained non-negative matrix factorization (CNMF)-defined ROIs (top) and ΔF/F traces (bottom) are exported. Scale bar = 100 µm. ( d ) Mice are head fixed and FOV under the GRIN lens imaged using the multiplexed lambda method. ( e ) Transformations are determined using anatomical background images to co-register the two imaging platforms. The transformations are applied to CNMF-defined ROIs. Scale bar = 100 µm. ( f ) Multispectral data are collected for each ROI (top) and an average spectral fingerprint for all ROIs is generated (bottom). Mean ±1.5 SD. Scale bar = 100 µm. ( g ) A linear unmixing model is applied to determine the fluorophore contribution for each ROI. Scale bar = 100 µm. ( i ) Neural activity is sorted by cell type. Scale bars = 20 ΔF/F (vertical), 20 s (horizontal).

Article Snippet: Because all imaging is performed through the implanted GRIN lens in vivo, Neuroplex is fully compatible with longitudinal designs, allowing users to assess fluorophore identity prior to behavioral testing, or to re-image the same cell populations across multiple time points.

Techniques: Injection, Imaging, Generated, Activity Assay

( a ) Multicolor image obtained through 1×4 mm silver-doped GRIN lens of the calibration slide highlighting the z-plane chromatic aberration. ( b ) Shift in z-focal plane as a function of excitation laser wavelength. Second-order polynomial R 2 =0.9926, n=5. ( c ) Orthogonal projection of multicolor image obtained through 1×4 mm silver-doped GRIN lens of the calibration slide. Intensity profile (below) of single ring for each excitation channel shows negligible chromatic shift along lateral axes. ( d ) Percent transmission through the GRIN lens as a function of excitation laser wavelength. Sixth order polynomial R 2 =0.9751, n=5. ( e ) Orthogonal projection of calibration slide imaged through 1×4 mm silver-doped GRIN lens overlaid (in cyan) with rectilinear grid lines. Substantial overlap of fluorescent rings from the grid indicates minimal field distortions. ( f ) Excerpt from ( e ) showing the rings focused in the sagittal plane (z=+20 µm), the circle of least confusion (z=0 µm), and the tangential focal plane (z=–17.5 µm). ( g ) Curvature of the Petzval field as a function of radial distance from center of the GRIN lens. Astigmatism results in three axially separated focal planes. Second order polynomial sagittal R 2 =0.9845, least confusion R 2 =0.8839, and tangential R 2 =0.7519, n=3. Scale bars = 100 µm.

Journal: eLife

Article Title: Functional imaging of nine distinct neuronal populations under a miniscope in freely behaving animals

doi: 10.7554/eLife.110277

Figure Lengend Snippet: ( a ) Multicolor image obtained through 1×4 mm silver-doped GRIN lens of the calibration slide highlighting the z-plane chromatic aberration. ( b ) Shift in z-focal plane as a function of excitation laser wavelength. Second-order polynomial R 2 =0.9926, n=5. ( c ) Orthogonal projection of multicolor image obtained through 1×4 mm silver-doped GRIN lens of the calibration slide. Intensity profile (below) of single ring for each excitation channel shows negligible chromatic shift along lateral axes. ( d ) Percent transmission through the GRIN lens as a function of excitation laser wavelength. Sixth order polynomial R 2 =0.9751, n=5. ( e ) Orthogonal projection of calibration slide imaged through 1×4 mm silver-doped GRIN lens overlaid (in cyan) with rectilinear grid lines. Substantial overlap of fluorescent rings from the grid indicates minimal field distortions. ( f ) Excerpt from ( e ) showing the rings focused in the sagittal plane (z=+20 µm), the circle of least confusion (z=0 µm), and the tangential focal plane (z=–17.5 µm). ( g ) Curvature of the Petzval field as a function of radial distance from center of the GRIN lens. Astigmatism results in three axially separated focal planes. Second order polynomial sagittal R 2 =0.9845, least confusion R 2 =0.8839, and tangential R 2 =0.7519, n=3. Scale bars = 100 µm.

Article Snippet: Because all imaging is performed through the implanted GRIN lens in vivo, Neuroplex is fully compatible with longitudinal designs, allowing users to assess fluorophore identity prior to behavioral testing, or to re-image the same cell populations across multiple time points.

Techniques: Transmission Assay

( a ) Shift in z-focal plane as a function of excitation laser wavelength in a 1×4 mm silver-doped GRIN lens. Second-order polynomial R 2 =0.9970. ( b ) Shift in z-focal plane as a function of excitation laser wavelength in 0.6×7 mm GRIN lenses doped with either silver or lithium. Second-order polynomials: Silver R 2 =0.9983, Lithium R 2 =0.9928. ( c ) Percent transmission through a 1×4 mm silver-doped GRIN lens as a function of excitation laser wavelength. Sixth-order polynomial R 2 =0.9926. ( d ) Percent transmission through 0.6×7 mm GRIN lenses doped with either silver or lithium as a function of excitation laser wavelength. Sixth-order polynomial: silver, R 2 =0.9979; lithium, R 2 =0.9549.

Journal: eLife

Article Title: Functional imaging of nine distinct neuronal populations under a miniscope in freely behaving animals

doi: 10.7554/eLife.110277

Figure Lengend Snippet: ( a ) Shift in z-focal plane as a function of excitation laser wavelength in a 1×4 mm silver-doped GRIN lens. Second-order polynomial R 2 =0.9970. ( b ) Shift in z-focal plane as a function of excitation laser wavelength in 0.6×7 mm GRIN lenses doped with either silver or lithium. Second-order polynomials: Silver R 2 =0.9983, Lithium R 2 =0.9928. ( c ) Percent transmission through a 1×4 mm silver-doped GRIN lens as a function of excitation laser wavelength. Sixth-order polynomial R 2 =0.9926. ( d ) Percent transmission through 0.6×7 mm GRIN lenses doped with either silver or lithium as a function of excitation laser wavelength. Sixth-order polynomial: silver, R 2 =0.9979; lithium, R 2 =0.9549.

Article Snippet: Because all imaging is performed through the implanted GRIN lens in vivo, Neuroplex is fully compatible with longitudinal designs, allowing users to assess fluorophore identity prior to behavioral testing, or to re-image the same cell populations across multiple time points.

Techniques: Transmission Assay