Journal: Neuroscience Bulletin

Article Title: A Two-Step GRIN Lens Coating for In Vivo Brain Imaging

doi: 10.1007/s12264-019-00356-x

Figure Lengend Snippet: Images of primary rat hippocampal neurons after 15 days in culture with coated and uncoated lenses. A Parylene-C-coated 1-mm diameter Go!Foton lenses. There was no parylene-C coating on the top end of the GRIN lens (arrow:coating interface). B Hippocampal neurons cultured with a coated lens maintained normal morphology. Left, coated lens; middle, neurons on the surface of lens (arrows); right, neurons near the lens. C Neurons cultured with an uncoated lens were characterized by the complete loss of neurites and changes in the cytoplasm. Left, uncoated lens; middle, neurons on the surface of lens (arrows); right, neurons near the lens. Scale bars, 100 μm.

Article Snippet: To determine whether the Go!Foton GRIN lens leached thallium ion into the solution, we soaked 8 uncoated lenses in 5 mL PBS for 20 days at room temperature.

Techniques: Cell Culture

Journal: Neuroscience Bulletin

Article Title: A Two-Step GRIN Lens Coating for In Vivo Brain Imaging

doi: 10.1007/s12264-019-00356-x

Figure Lengend Snippet: Two steps of coating enable successful in vivo imaging using Go!Foton lenses. A Neither active neurons nor blood vessels were observed under a Go!Foton lens without coating. B Active neurons (arrowhead) and blood clots (arrow) were observed under a GRIN lens coat with parylene-C alone. C Both active neurons (arrowhead) and blood vessels (arrow) were observed under GRIN lenses coated with both parylene-C and 50 μg/mL fibronectin. D Both active neurons (arrowhead) and blood vessels (arrow) were observed under a GrinTech lens. Scale bar, 100 μm.

Article Snippet: To determine whether the Go!Foton GRIN lens leached thallium ion into the solution, we soaked 8 uncoated lenses in 5 mL PBS for 20 days at room temperature.

Techniques: In Vivo Imaging

Journal: Neuroscience Bulletin

Article Title: A Two-Step GRIN Lens Coating for In Vivo Brain Imaging

doi: 10.1007/s12264-019-00356-x

Figure Lengend Snippet: Comparison of imaging performance. A–C Representative standard deviation projection images from miniScope recording via GRIN lenses coated with parylene-C and fibronectin at 100 μg/mL (Group 1) (A), 50 μg/mL (Group 2) (B), and 25 μg/mL (Group 3) (C). D Representative standard deviation projection image from miniScope recording via a GrinTech GRIN lens (Group 4). E Average ∆F/F of all the neurons from each group. Group 1: 2.46% ± 0.06%, 96 neurons from two mice; Group 2: 4.50% ± 0.13%, 224 neurons from two mice; Group 3: 5.55% ± 0.34%, 100 neurons from two mice; Group 4: 4.85% ± 0.14%, 366 neurons from three mice. ****P < 0.0001, one-way ANOVA and Tukey’s post hoc test. Histogram bars represent the mean value for all neurons, with error bars representing SEM. Scale bar, 100 μm.

Article Snippet: To determine whether the Go!Foton GRIN lens leached thallium ion into the solution, we soaked 8 uncoated lenses in 5 mL PBS for 20 days at room temperature.

Techniques: Comparison, Imaging, Standard Deviation

Journal: bioRxiv

Article Title: Multimodal alignments of in vivo imaging and spatial biology datasets at cellular resolution

doi: 10.64898/2026.04.28.719500

Figure Lengend Snippet: A) We evaluated the field curvature of a GRIN lens (1 mm diameter, 4.38 mm length; 1050-006242, Inscopix) used for two-photon Ca 2+ imaging in the dorso-medial striatum ( Methods ), showing a need to align neurons across multiple ex vivo confocal slices as in . Left : Cross-sectional projections from volumetric image stacks acquired using two-photon microscopy through a GRIN lens to image a fluorescent glass coverslip. The image of the glass surface has relatively low axial resolution but is also quite flat within a ∼150 μm radius from the optical axis. Scale bars: 100 μm (X and Y lateral dimensions) and 50 μm (Z, axial dimension). Middle : Color plots showing the axial displacement of the image of the slide as a function of the lateral displacement from the optical axis, determined as in and . For each (X, Y) position, we determined the axial displacement of the image of the slide by performing a Gaussian fit to the image brightness values as a function of Z and then taking the Z position corresponding to the peak of the Gaussian. Scale bar: 200 μm; Right : Mean ± s.d. axial displacement of the two-photon image of the fluorescent slide, plotted as a function of the radial displacement from the optical axis, averaged over all azimuthal angles. The vertical dashed line marks 150 μm radial displacement from the optical axis; we used the portion of the in vivo imaging field-of-view lying within radial displacements less than this. B) Top : Maps of cells obtained from in vivo (green) and ex vivo (magenta) datasets, showing that different subsets of cells observed in vivo through a GRIN lens are matched with counterparts found in several different axial planes in the ex vivo image stack (image planes were acquired with an axial spacing of 2 μm; shown are planes 4 μm apart). Scale bar: 100 μm. Bottom : Distributions of Soma-print scores for pairs of best-matched (orange) or 2 nd -best-matched cell pairs (blue), along with parametric fits and semi-logarithmic versions ( insets ) of the plots, shown in the same format as in for each of the image slices in the top row. C) Color plot for the same dataset as in B , showing the best Soma-print scores for all 414 cells found in vivo, when matched using the 2D Soma-print algorithm to the data from individual axial planes in the ex vivo image stack. The 3D algorithm then identifies for each cell the axial plane with the maximum Soma-print score. D) Corresponding in vivo and ex vivo images of spiny projection neurons from the dorsal medial striatum of a Drd1a-Cre ✕ Ai14 mouse. We labeled cells and acquired images in the same manner as in , except that here the in vivo two-photon Ca 2+ imaging was performed through a microprism implanted in the striatum. Rectangles enclose example subregions with neurons that can be readily tracked by eye across the image panels shown in F . Scale bar: 100 μm. E) Example traces of Ca 2+ activity from neurons imaged in D via the microprism of an awake resting mouse. F) Magnified views of the regions enclosed by the color-corresponding rectangles in D . Within the image panel for each subregion, image frames are arranged from left to right to show the in vivo and HCR-FISH Round 1 data, respectively. Scale bar: 20 μm. G) Overlay of cell pairs matched by the Soma-print algorithm across in vivo (green) and reconstructed ex vivo (magenta) cell maps for the data of D , shown in the same format as in B . Scale bar: 100 μm. H) Distributions of Soma-print scores for pairs of best-matched cell or 2 nd -best-matched cell pairs computed for the image of D . Data and parametric fits are shown in the same format as in B.

Article Snippet: 4 weeks after the cannula implantation, we assessed Ca 2+ indicator expression in the dorsal striatum by inserting a GRIN lens (1 mm diameter, 4.38 mm length; 1050-006242, Inscopix) into the cannula and used a custom-built two-photon microscope equipped with a 0.8 NA microscope objective lens (CFI75 LWD 16× W, Nikon) to image the striatum while the mouse was head-fixed and placed on a running wheel.

Techniques: Imaging, Ex Vivo, Microscopy, In Vivo Imaging, In Vivo, Labeling, Activity Assay

Journal: bioRxiv

Article Title: Multimodal alignments of in vivo imaging and spatial biology datasets at cellular resolution

doi: 10.64898/2026.04.28.719500

Figure Lengend Snippet: A) Corresponding images from the dorsal medial striatum of a Drd1a-Cre ✕ Ai14 mouse, in which spiny projection neurons (SPNs) expressing the D1-dopamine receptor are labeled with red fluorescent tdTomato. Local injection of AAV2/PHP.eB-CaMKII-jGCaMP8m in the striatum allowed viral expression of GCaMP8m and Ca 2+ imaging in both major classes of SPNs, irrespective of whether they expressed D1- or D2-dopamine receptors. Left : Example image taken by two-photon microscopy via a GRIN microlens in a mouse at liberty to run in place on a wheel, averaged over 9,000 image frames acquired at 30 fps. Right : Confocal fluorescence image reconstructed by the 3D Soma-print algorithm from the first round of postmortem HCR-FISH images, showing fluorescent labeling of mRNA encoding GCaMP8m and tdTomato. Dashed white ellipses enclose subregions with cells that can be readily tracked by eye across the image panels. Scale bar: 100 μm. B) Example traces of Ca 2+ activity from neurons imaged in A via the GRIN lens. C) We used the sparsely labeled set of red (tdT + ) fluorescent cells in A to evaluate the quality of cell pair matching with the Soma-print algorithm. Using visually determined matches from the sparsely labeled subset as the ground truth, the precision and recall values for matches determined with the algorithm were 90% ± 1% and 95 ± 2%, respectively (mean ± s.e.m. over n=3 image pairs). (See for definitions of alignment precision and recall). D) Map of 333 cells matched with the 3D Soma-print algorithm out of a total of 414 cells from one in vivo imaging plane (80% sensitivity), color-coded by the cells’ registered axial locations in the ex vivo z-stack of images. Scale bar: 100 μm. E) Image overlay of cell pairs matched by the Soma-print algorithm, D , across the in vivo (green) and reconstructed ex vivo (magenta) cell maps for the data of A . Overlapping pixels in the two maps are shown in white. Scale bar: 100 μm. F) Distributions of Soma-print scores for pairs of best-matched cell pairs (orange) or 2 nd -best-matched cell pairs (blue), computed for the image of E . Data are shown in the same format as in . G) Schematic of the optomechanical protocol used to align the miniature two-photon microscope (TRANSVISTA) for imaging in a freely behaving animal. (1) We first aligned the microscope’s optical axis and the mouse’s implant while the animal was head-fixed. Using a 5-axis mechanical stage and a laser pointer, we used the light reflected off the cranial window to align the mouse relative to the illumination axis of the laser. We then used a 3-axis mechanical holder to co-align the mini-scope and its headpiece to this same axis. (2) After identifying a satisfactory field-of-view for two-photon imaging, we glued the lower baseplate of the headpiece to the mouse while it was head-fixed. (3) After the glue dried, we detached the microscope from the lower baseplate and returned the mouse to its home cage. Prior to subsequent imaging sessions, we reconnected the upper and lower baseplates to ensure a precise return to the same field-of-view. After in vivo imaging was completed, we followed the tissue processing and sectioning steps of or . H) Corresponding pair of example images of mouse motor cortical layer 2/3 pyramidal cells that virally expressed GCaMP8s. Left : Time-averaged image taken during active mouse behavior in an open field enclosure, averaged over 6,000 image frames taken at 9.2 fps ( Supplementary Video 1 ). Right : Confocal fluorescence image from the first round of HCR-FISH imaging, showing nuclear DAPI staining and fluorescent labeling of mRNAs encoding GCaMP8s, SST, Cux2, and Slc17a7. The image is a sum of the image slices taken of 3 consecutive axial planes spaced 2 μm apart. Dashed white ellipses enclose subregions with neurons that can be readily tracked by eye across the image panels. Scale bar: 100 μm. I) Top: Example trace of the mouse’s running speed in the open field enclosure. Bottom : Ca 2+ activity traces from 10 example neurons from panel H . J) Distributions of Soma-print scores for pairs of best-matched (orange) or 2 nd -best-matched cell pairs (blue), for the data of H . Data are shown in the same format as in F and . 211 of the 274 neurons (sensitivity: 77%) found in one plane in vivo were successfully matched to a cell found in the ex vivo image, each with a relative likelihood of an incorrect match of <0.05.

Article Snippet: 4 weeks after the cannula implantation, we assessed Ca 2+ indicator expression in the dorsal striatum by inserting a GRIN lens (1 mm diameter, 4.38 mm length; 1050-006242, Inscopix) into the cannula and used a custom-built two-photon microscope equipped with a 0.8 NA microscope objective lens (CFI75 LWD 16× W, Nikon) to image the striatum while the mouse was head-fixed and placed on a running wheel.

Techniques: Expressing, Labeling, Injection, Imaging, Microscopy, Fluorescence, Activity Assay, In Vivo Imaging, Ex Vivo, In Vivo, Staining