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Data acquisition software

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The Inscopix data acquisition software is a core component of the Inscopix system. It provides the essential functionality to record, visualize, and analyze neural activity data acquired through Inscopix's miniature fluorescence microscopes.

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Lab products found in correlation

Data processing software, by Inscopix (2 mentions) Nvoke2, by Inscopix (2 mentions) Nvista 3, by Inscopix (1 mentions) Matlab, by MathWorks (1 mentions) Data processing software idps, by Inscopix (1 mentions) Nvista 2, by Inscopix (1 mentions)

7 protocols using data acquisition software

1

In Vivo Pulsatile LH Secretion

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Images were acquired using a single-photon epifluorescence microscope (nVoke miniaturized microscope; Inscopix) and Inscopix Data Acquisition Software. Images were captured at 10 frames per second (10 Hz) with 0.8 to 1 mW of LED (light emitting diode) power and a gain of 4. Images were collected for a total of 60 min per mouse. To assess LH pulsatile secretion, serial 3-µL blood samples were collected from the tail tip of freely moving mice every 3 or 4 min over the 60-min imaging period and diluted in 57 µL of 0.1M PBS with 0.02% Tween 20. Blood samples diluted in PBS-Tween 20 were immediately frozen on dry ice and then stored at −20 C until measurement of LH levels using enzyme-linked immunosorbent assay (ELISA).
Moore A.M., Coolen L.M, & Lehman M.N. (2022). In vivo imaging of the GnRH pulse generator reveals a temporal order of neuronal activation and synchronization during each pulse. Proceedings of the National Academy of Sciences of the United States of America, 119(6), e2117767119.
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2

Miniscope Data Preprocessing and Filtering

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Miniscope data were acquired using the Inscopix Data Acquisition Software as 2x down-sampled .isxd files. Preprocessing and motion correction was performed using the Inscopix Data Processing Software. Briefly, raw imaging data was cropped, 2x down-sampled, median filtered and motion corrected. A spatial band-pass filter was then applied to remove out of focus background. The filtered imaging data was temporal down-sampled to 10Hz and exported as a .tiff image stack.
Yang B., Karigo T, & Anderson D.J. (2022). TRANSFORMATIONS OF NEURAL REPRESENTATIONS IN A SOCIAL BEHAVIOR NETWORK. Nature, 608(7924), 741-749.
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3

Miniature Fluorescence Microscopy for Calcium Imaging in Behaving Mice

Cited 1 time
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For time-lapse imaging in behaving mice we used an integrated miniature fluorescence microscope (nVista 3.0, Inscopix) as previously described26 (link). At least two weeks after the glass guide tube implantation, we inserted a microendoscope consisting of a metal guide cannula (~3.1 mm length, 1.8 mm outer diameter) and a single gradient refractive index (GRIN) lens (4.0 mm length, 1.0 mm diameter) into the implanted glass tube and examined Ca2+ indicator expression in the operated mice (Inscopix data acquisition software, Inscopix). We then affixed the microendoscope within the glass guide tube using ultraviolet-curing adhesive (Flow-It A3, Pentron). Next, we attached the miniature microscope’s magnetic base plate to the dental acrylic surface with the ultraviolet-curing adhesive. At least a day later, the mice were habituated wearing the miniature microscope in their home cage for 30 minutes for 4–5 days. To record mouse behavior in the home cage, we used an overhead monochrome camera (GigE Vision, Basler AG), which we synchronized with the miniature microscope. Ca2+ imaging was performed at 10 Hz. Imaging sessions consisted of 18-min-long trials.
Shoob S., Buchbinder N., Shinikamin O., Gold O., Baeloha H., Langberg T., Zarhin D., Shapira I., Braun G., Habib N, & Slutsky I. (2023). Deep brain stimulation of thalamic nucleus reuniens promotes neuronal and cognitive resilience in an Alzheimer’s disease mouse model. Nature Communications, 14, 7002.
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4

Calcium Imaging Data Acquisition and Processing

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Inscopix data acquisition software (IDAS; Inscopix) was used to acquire TIFF images of fluorescence dynamics at 20 frames per second. Calcium frame acquisition was triggered via Ethovision XT (v10) and began at the onset of the session. Calcium acquisition was automatically terminated after 30 minutes.
Inscopix data processing software (IDPS; Inscopix) was used to preprocess Ca2+ data from each imaging session as previously described 53 (link),54 . Briefly, for each day, calcium imaging data from ad libitum and food deprived test days were down-sampled temporally (2x temporal bin) and spatially (4x spatial bin) and rigid motion correction was applied. After preprocessing, putative single neuron activity was segmented using Constrained Non-negative Matrix Factorization for Endoscopic data (CNMFe) using custom MATLAB (MathWorks, Natick, MA, USA) scripts (https://github.com/BruchasLab). Individual putative striatal neurons were tracked between ad libitum and food deprived sessions using CellReg (cite PMID: 29069591). For each mouse the spatial correlation registration threshold performed best, and thresholds were determined by the algorithm. Final registration utilized the probabilistic model with a P_same (probability of cells being the same) > 0.6 for all mice.
Castro D.C., Oswell C.S., Zhang E.T., Pedersen C.E., Piantadosi S.C., Rossi M.A., Hunker A., Guglin A., Morón J.A., Zweifel L.S., Stuber G.D, & Bruchas M.R. (2021). An endogenous opioid circuit determines state-dependent reward consumption. Nature, 598(7882), 646-651.
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5

Inscopix Cell Identification Protocol

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Before admission to the experiment, the Minsicope was magnetically attached to each animal’s implant for habituation and streamed using the Inscopix Data Acquisition Software. If many cells could be observed during spontaneous behavior in the home cage, the mouse was admitted. If only a few cells were visible, the session was recorded and analyzed in the Inscopix Data Processing Software (IDPS) to determine the number of observable cells. If an animal had >20 identifiable cells, they were admitted into the study. Others were euthanized.
Rogers S.A., Heller E.A, & Corder G. (2024). Psilocybin-enhanced fear extinction linked to bidirectional modulation of cortical ensembles. bioRxiv.
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6

Elevated Platform Exploration Assay

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Mice were connected to the nVoke2 (Inscopix) system and recorded with the Inscopix data acquisition software with a 20-Hz sampling rate while behaviorally recorded simultaneously from above using a camera (The Imaging Source) that is controlled by ANY-maze (v5.23, Stoelting) and sampled up to 20 Hz. The mice were then placed in the enclosed center of the elevated platform and recorded while freely moving for 5 min. The elevated platform is constructed by completely blocking the entrance of the closed arms of an EPM (arms with 7.5 cm in width, 30 cm in length separated by a center that is 7.5 cm in width and length and enclosed by 60-cm-tall cardboard pieces on the two sides not connected to the arms). This elevated platform maximizes and forces the recorded mice to explore the anxiogenic exposed open edges. The larger dimensions of this platform also provided more room for the recorded mice to maneuver.
Li Z., Rizzi G, & Tan K.R. (2021). Zona incerta subpopulations differentially encode and modulate anxiety. Science Advances, 7(37), eabf6709.
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7

Miniscope-based Fear Conditioning

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Implanted were checked bi-weekly until the area below the lens have cleared and GCaMP6m labeled cells can be visualized. To do so, mice were held by the head-bar on a custom-built running wheel while the miniscope (Inscopix) is attached. ZI calcium transients were recorded by the nVoke2 and nVista2 (Inscopix) systems and visualized through the Inscopix Data Acquisition Software (IDAS). Once cells could be visualized, mice were individually handled and habituated to the experimental room (5 mins per day for 3 consecutive days). Following the last handling day, mice were subjected to a 7-day fear conditioning protocol (pre-conditioning, 5 conditioning days, and test day). On each day, the miniscope is first attached and mice were then placed into either a plexiglass box (20cm wide, 25cm long, 15cm tall) covered with polka-dots (context A, pre-conditioning/test days, cleaned with 1% acetic acid) or a different (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission.
Li Z., Rizzi G., & Tan K.R. (2021). Zona Incerta activity dynamics underlying associative fear learning and fear generalization.
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