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Synapse software

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Synapse software is a tool for data acquisition, visualization, and analysis. It provides a platform for researchers and scientists to record, process, and interpret experimental data from various sources.

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Lab products found in correlation

Mf470f3, by Thorlabs (2 mentions) Mf405fp1, by Thorlabs (2 mentions) Digital optical power meter, by Thorlabs (2 mentions) Rzx10 lux, by Tucker-Davis Technologies (2 mentions) Minicube, by Doric (2 mentions) Dc4100, by Thorlabs (2 mentions) 6 port minicube, by Doric (2 mentions) 4 port minicube fmc4, by Doric (1 mentions) Model dc4104, by Thorlabs (1 mentions) Data acquisition system, by Tucker-Davis Technologies (1 mentions) Premiere pro, by Adobe (1 mentions) Led driver, by Doric (1 mentions) Prism 7, by GraphPad (1 mentions) Rz10x, by Tucker-Davis Technologies (1 mentions) Led driver, by Thorlabs (1 mentions) Med pc 5 software, by Med Associates (1 mentions) 400um core, by Doric (1 mentions) Fiber optic rotary joint, by Doric (1 mentions) Fluorescence minicube, by Doric (1 mentions)

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Synapse (16 citations) SYNAPSE recording software (SYSTEM3, (2 citations)

18 protocols using synapse software

1

Fiber Photometry for Neurotransmitter Dynamics

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Fiber photometry was performed as described previously2 (link). Mice were attached via an optical fiber (400μm core, 0.48NA; Doric Lenses), which was connected to a Doric 4-port minicube (FMC4, Doric Lenses). Dual color LED light (470nm for GRAB-DA stimulation, ThorLabs #MF470F3; 405nm for artifact control fluorescence, ThorLabs #MF405FP1) was delivered through the fiberoptic cannula into the brain at 10–30μW (ThorLabs, LED Driver Model DC4104). Photon emissions were passed through a dichroic mirror and 5000–550nm cult filter, then detected by a femtowatt silicon photoreceiver (Newport, Model 2141). Analog signals were demodulated and recorded with an RZ5 processor and Synapse Software (Tucker Davis Technologies). Prior to each recording session, 470nm light was passed through the patch cord for at least 4h to reduce autofluorescence.
Mice were connected to the patch cord with the LEDs on in the operant chambers for at least 10 min prior to experimental sessions to allow for habituation. All recording sessions began with a 10 min baseline period. Operant training sessions as described above were typically 60min, but allowed to extend longer (no more than 120min) if the mouse had started to acquire the task but was not yet exhibiting consistent accurate performance.
Holly E.N., Davatolhagh M.F., España R.A, & Fuccillo M.V. (2021). Striatal low-threshold spiking interneurons locally gate dopamine. Current biology : CB, 31(18), 4139-4147.e6.
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2

In Vivo Optogenetic Fiber Photometry System

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Mice were attached via an optical fiber (400 mm core, 0.48 NA; Doric Lenses) to a Doric 4-port minicube (FMC4, Doric Lenses). Blue (470 nm wavelength for GCaMP6f stimulation, ThorLabs #MF470F3) and violet (405 nm wavelength for artifact control fluorescence, ThorLabs #MF405FP1) LED light was delivered to the brain at 10–100 mW (LED driver: Thor Labs, Model DC4104). Emissions passed through a dichroic mirror, a 500–550 nm cut filter and were then detected by a femtowatt silicon photoreceiver (Newport, Model 2151). Analog signals were demodulated and recorded (Tucker Davis Technologies, RZ5 processor and Synapse Software). To reduce the autofluorescence of patchcord fibers, 470nm light was passed through for a minimum of 4 hours prior to recording. Mice were always hooked up to the optical fiber with the LEDs on for at least 10min prior to recordings began. Once signal collection recordings were started, there was a baseline period of at least 6 min prior to the introduction of any stimuli or the initiation of any task in the operant chamber.
Holly E.N., Davatolhagh M.F., Choi K., Alabi O.O., Cifuentes L.V, & Fuccillo M.V. (2019). Striatal Low-Threshold Spiking Interneurons Regulate Goal-Directed Learning. Neuron, 103(1), 92-101.e6.
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3

Multimodal Neurophysiological Recording Protocol

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Neurophysiological and EMG data were collected using a data acquisition system (Tucker-Davis Technologies, Gainsville, FL) with sampling rates of approximately 25 and 1.5 kHz, respectively. Neural data were collected simultaneously from two cortical locations using 16-site, 3 or 5 mm silicon-iridium electrodes (A1x16-3 mm-100-177-A16 or A1x16-5 mm-100-177-A16; NeuroNexus, Ann Arbor, MI). Before insertion, electrodes were coated with a fluorescent dye (DiI; Invitrogen, Waltham, MA) for later confirmation of placement. A chlorinated silver wire (0.25 mm in diameter; Medwire, Mt. Vernon, NY) was inserted into occipital cortex and used as both reference and ground. Neural data were recorded and visualized using Synapse software (Tucker-Davis Technologies). Video was collected using a BlackFly-S camera (100 fps) and SpinView software (FLIR Integrated Systems, Wilsonville, OR). To enable synchronization of the video and electrophysiological records, an LED was positioned within the camera frame and was programmed to flash once every 3 s (Dooley et al., 2021 (link)).
Gómez L.J., Dooley J.C, & Blumberg M.S. (2023). Activity in developing prefrontal cortex is shaped by sleep and sensory experience. eLife, 12, e82103.
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4

In-Vivo Fiber Photometry Recordings in Mice

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We anesthetized animals using 2% isoflurane and placed them in a stereotaxic frame. Mice were implanted with a fiber optic probe (400 μM diameter, 0.39NA; RWD Life Sciences) in the PBN (−5.2mm AP, +1.5mm ML, −2.2 to −2.5mm DV) during the same surgery they were injected with the viral construct and the head plate was implanted. The mice were given 3 weeks to recover and to allow for viral expression in their home cage.
For recordings, the fiber optic probe was connected to an RZX10 LUX fiber photometry processor running Synapse software (Tucker-Davis Technologies) through a Doric mini cube (Doric Lenses). LEDs at 465 nm and 405 nm were used for GCaMP excitation and isosbestic control, respectively. LED power was calibrated weekly using a digital optical power meter (Thor Labs).
Smith J.A., Ji Y., Lorsung R., Breault M.S., Koenig J., Cramer N., Masri R, & Keller A. (2023). Parabrachial nucleus activity in nociception and pain in awake mice. bioRxiv.
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5

Chronic Thalamic ECoG Recordings

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To control for circadian rhythms, animals were housed using a regular light/dark cycle, and recordings performed between 7:00 AM and 7:00 PM. Prior to acquisition of multi-site EcoG recordings (Figs. 4, 5, S6), mice were allowed to recover for at least one week. EcoG signals were recorded using RZ5 via Synapse software (Tucker Davis Technologies) and sampled at 1221 Hz. Animals were continuously monitored during recordings using a video camera that was synchronized to the signal acquisition via RZ5 (43 (link)).
Chronic, continuous EcoG recordings (Fig. 6, table S9) were acquired using wireless telemetry devices (PhysioTel HD-X02 implants, Data Sciences International) and sampled at 500 Hz via Ponemah software (DSI). 24/7 recordings were performed for one-week periods (168 hours) at the following timepoints: 1, 3, 5 and 7 weeks after thalamic astrogliosis (Fig. 6C), and 7 weeks after thalamic astrogliosis with GAT-3 enhancement (Fig. 6D). Acquisition started immediately following implantation, as the wireless devices allow mice to remain in their home cages.
Cho F.S., Vainchtein I.D., Voskobiynyk Y., Morningstar A.R., Aparicio F., Higashikubo B., Ciesielska A., Broekaart D.W., Anink J.J., van Vliet E.A., Yu X., Khakh B.S., Aronica E., Molofsky A.V, & Paz J.T. (2022). Enhancing GAT-3 in thalamic astrocytes promotes resilience to brain injury in rodents. Science translational medicine, 14(652), eabj4310.
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6

Fiber Photometry for Calcium Imaging

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Fiber photometry was performed as previously described56 ,57 . Briefly, mice were allowed to habituate to the fiber patch cord in their home cage for approximately 5 min before each behavior test. GCaMP fluorescence and isosbestic autofluorescence signals were excited by the fiber photometry system (Doric Lenses) using two sinusoidally modulated 473 nm (211 Hz) and 405 nm (531 Hz) LEDs (DC4100, ThorLabs). Both LEDs were combined via a commercial Mini-cube fiber photometry apparatus (Doric Lenses) into a fiber patch-cord (400 μm core, 0.48 NA) connected to the brain implant in each mouse. The light intensity at the interface between the fiber tip and the animal was adjusted from 10 to 20 μW (but was constant throughout each test session for each mouse). An RZ5P fiber photometry acquisition system with Synapse software (Tucker-Davis Technologies) collected and saved real-time demodulated emission signals and behavior relevant TTL inputs. For each trial, GCaMP signals (F473 nm) were compared with autofluorescence signals (F405 nm) to control for movement and bleaching artefacts. Signal data was de-trended by first applying a least-squares linear fit to produce Ffitted 405 nm, and dF/F was calculated as (F473 nm – Ffitted 405 nm)/Ffitted 405 nm. All GCaMP signal data is presented as the z-score of the dF/F from baseline (pre-CS) segments.
Ma J., du Hoffmann J., Kindel M., Sofia Beas B., Chudasama Y, & Penzo M.A. (2021). Divergent projections of the paraventricular nucleus of the thalamus mediate the selection of passive and active defensive behaviors. Nature neuroscience, 24(10), 1429-1440.
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7

Calcium and Dopamine Imaging Protocol

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GCaMP6f, GCaMP7f or dLight1.1 were excited by amplitude modulated signals from two light-emitting diodes (465- and 405-nm isosbestic control, DORIC) reflected off dichroic mirrors (6-port minicube, DORIC) and coupled into a single FP optic fiber (400um-core, NA 0.48, DORIC). Sensor signals and isosbestic control emissions were returned through the same optic fiber and acquired using a femtowatt photoreceiver (Newport), digitized at 1017 Hz, and recorded by a real-time signal processor (RZ5P, Tucker Davis Technologies, RRID:SCR_006495). Behavioral and event timestamps were digitized in Synapse software (Tucker Davis Technologies) by TTL inputs from Med-PC, Any-Maze, or manual triggers. Power of light used for imaging (<0.2 mW) is ~2 orders of magnitude less than used for laser stimulation (10 mW), and the distance between the brain sites of stimulation and calcium or DA imaging was >3.5 mm.
Faget L., Oriol L., Lee W.C., Zell V., Sargent C., Flores A., Hollon N.G., Ramanathan D, & Hnasko T.S. (2024). Ventral pallidum GABA and glutamate neurons drive approach and avoidance through distinct modulation of VTA cell types. Nature Communications, 15, 4233.
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8

Video Recording of Mouse Behavior

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We video recorded mice via USB cameras (1080p USB webcam, Angetube), using either iSpy software (iSpyConnect.com) or Synapse software (Tucker-Davis Technologies). We used Adobe Premiere Pro (Adobe Creative Cloud) to generate representative videos. The speed of the representative videos was accelerated x30 or x100, as indicated.
Crowell D.N., Kadlecek A.T., John M.C, & Amasino R.M. (1990). Cytokinin-induced mRNAs in cultured soybean cells.. Proceedings of the National Academy of Sciences of the United States of America, 87(22), 8815-8819.
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9

Fiber Photometry for Calcium Imaging

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Fiber photometry was performed as previously described56 ,57 . Briefly, mice were allowed to habituate to the fiber patch cord in their home cage for approximately 5 min before each behavior test. GCaMP fluorescence and isosbestic autofluorescence signals were excited by the fiber photometry system (Doric Lenses) using two sinusoidally modulated 473 nm (211 Hz) and 405 nm (531 Hz) LEDs (DC4100, ThorLabs). Both LEDs were combined via a commercial Mini-cube fiber photometry apparatus (Doric Lenses) into a fiber patch-cord (400 μm core, 0.48 NA) connected to the brain implant in each mouse. The light intensity at the interface between the fiber tip and the animal was adjusted from 10 to 20 μW (but was constant throughout each test session for each mouse). An RZ5P fiber photometry acquisition system with Synapse software (Tucker-Davis Technologies) collected and saved real-time demodulated emission signals and behavior relevant TTL inputs. For each trial, GCaMP signals (F473 nm) were compared with autofluorescence signals (F405 nm) to control for movement and bleaching artefacts. Signal data was de-trended by first applying a least-squares linear fit to produce Ffitted 405 nm, and dF/F was calculated as (F473 nm – Ffitted 405 nm)/Ffitted 405 nm. All GCaMP signal data is presented as the z-score of the dF/F from baseline (pre-CS) segments.
Ma J., du Hoffmann J., Kindel M., Sofia Beas B., Chudasama Y, & Penzo M.A. (2021). Divergent projections of the paraventricular nucleus of the thalamus mediate the selection of passive and active defensive behaviors. Nature neuroscience, 24(10), 1429-1440.
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10

Calcium-dependent GCaMP6 Fluorescence Imaging

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Changes in the calcium-dependent GCaMP6 fluorescence (465 nm) were compared with a 405-nm isosbestic control, to provide internal control for movement and auto bleaching artefacts. Fluorescence measurements were recorded employing Synapse software (v.95-43718P, Tucker-Davis Technologies) and analysed using a custom MATLAB script. The fluorescence signal was defined as ratio of fluorescence at 465 nm to the fluorescence measured at 405 nm. For i.p. hormone injection and food exposure experiments, the median of the baseline recording before treatment was defined as F0. The post-treatment signal (dF/F0) was calculated by comparing the fluorescence signal with the pretest baseline (dF(t)/F0 = (F(t) − F0)/F0). For all experiments photobleaching correction was not necessary, due to the low laser power used and optimized patchcords, which prevent photobleaching of the optical system. In the figures, dF/F(%) represents the mean dF(t)/F0 × 100.
Porniece Kumar M., Cremer A.L., Klemm P., Steuernagel L., Sundaram S., Jais A., Hausen A.C., Tao J., Secher A., Pedersen T.Å., Schwaninger M., Wunderlich F.T., Lowell B.B., Backes H, & Brüning J.C. (2021). Insulin signalling in tanycytes gates hypothalamic insulin uptake and regulation of AgRP neuron activity. Nature Metabolism, 3(12), 1662-1679.
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