Fluorescence Miniscope Solutions
Fluorescence Miniscope system is a precise method for imaging individual cell activity, specifically in freely-behaving animals. Unlike two-photon and confocal microscopy, which requires head-fixation or anesthesia, miniaturized microscopy enables studying unrestrained behavior during recordings. This is made possible by directly attaching a small, lightweight microscope to the animal’s head.
This technique requires expressing genetically encoded fluorophore indicators, such as GCaMP, dLight, and GRAB-Ach, into the target brain region. These indicators fluoresce when they bind specific molecules (e.g., dopamine, acetylcholine, calcium ions), serving as a proxy for neuronal activity. Next, a microscope cannula is implanted above the targeted brain area and later connected to the microscope body during recording sessions. By measuring fluorescence emission levels at high-temporal-rate from the brain tissue, the miniaturized microscope allows researchers to indirectly quantify neuronal activity in real time.
Since 2014, Doric Lenses has been among the leaders in the development of fluorescence miniscope systems and provides a comprehensive, all-in-one solution covering everything from the implant to the processed data: including imaging cannulas, microscope body, rotary-Joint, Fluorescence Microscope Driver, and data analysis solution (DanseTM). All Doric systems are fully compatible and perfectly synchronized with Doric’s optogenetics tools and behavior acquisition cameras (Behavior Cameras/CamLoop), ensuring a seamless workflow with continuous support for researchers.
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Surface Miniscope – Specifically designed for imaging superficial brain structures including all cortical areas.
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Deep Brain Miniscope – Optimized for all depth imaging including the deep brain structures, with the flexibility to also be used for surface area imaging.
See image below, which categorizes all Doric fluorescence miniscope systems:
Surface Miniscope
The Surface Miniscope is designed for imaging superficial brain regions located up to 150 mm deep, such as the Visual Cortex and Prefrontal Cortex. These microscopes are combined with a cranial window above the region of interest, which then connects to the microscope body via a snap-in connection. This cranial window design offers two key advantages:
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Reduced Surgery invasiveness – A significantly easier and less invasive procedure, addressing one of the most challenging steps in miniature microscopy.
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Superior Signal Quality – Larger diameter optical components provide higher image resolution across the entire field of view (FOV).
Surface Miniscope set includes the following versions:
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[Snap-in (SFMB-S)] → 1-color imaging (green or red fluorescence)
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[OSFM-S] → 1-color (green fluorescence) imaging with optogenetics (yellow-red wavelength)
OR 1-color (red fluorescence) imaging with optogenetics (blue wavelength)
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[2CFM-S] → 2-color imaging (green and red fluorescence)
The 1-color + optogenetics microscope (OSFM-S) is capable of providing up to 55 mW / mm2 of yellow-red wavelength light (580-640 nm pulsed or continuous) at the tip of the implant. This high-power output ensures efficient activation of yellow-red activated opsins, such as Halorhodopsin, which can be challenging to stimulate effectively.
Despite advantages, the larger optical lenses used in surface Miniscope systems are not suitable for deep brain imaging, as they may cause significant tissue damage if intruded deeply in brain. Even though specific custom configurations are proposed for imaging deeper layers of cortex and hippocampus using Surface Miniscope, usually a dedicated solution for deep structures imaging is required.
Deep brain Miniscope
Deep brain Miniscope solution is designed to record neural activity from structures located deep within the brain that cannot be accessed using the SURFACE Miniscope. These include regions such as the Substantia Nigra, Hypothalamus, and Parabrachial Nucleus, among many others.
Deep brain Miniscope has a distinct optical design which requires GRIN lens (thin rod-like lens) implantation for imaging purposes. To simplify the surgery and ensure an efficient optical alignment, the GRIN lens is integrated into an imaging cannula.
This microscope set includes the following versions:
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[eTFMB3] → 1-color imaging (green or red fluorescence)
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[eTOSFM3] → 1-color imaging (green fluorescence) with optogenetics (yellow-red wavelength) OR 1-color imaging (red fluorescence) with optogenetics (blue wavelength)
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[2CFM-L] → 2-color imaging (green and red fluorescence)
The first two Deep brain Miniscopes, 1-color (eTFMB3) and 1-color+optogenetics (eTOSFM3), are also known as Twist_on microscopes. This name comes from the connection mechanism to the cannulas (no pressure on the skull during connection, no tools required). They are also referred to as eFocus in the literature because they contain an embedded electronically adjustable lens inside the microscope body. Such electronic focus can be adjusted in the Doric Neuroscience Studio (DNS) software with a depth movement range of 300 µm, enabling remote focus adjustments between sessions and ensuring optimal imaging quality. The efocus feature provides a way to track the same cells over time and improves fluorescence signal and spatial resolution
The 1-color + optogenetics microscope (eTOSFM3) provides up to 55 mW / mm2 of yellow-red wavelength light (580-640 nm pulsed or continuous) at the tip of the implant. This high-power output ensures efficient activation of yellow-red activated opsins, such as Halorhodopsin that have higher activation thresholds.
Lastly, the 2-color microscope (2CFM-L), features two separate integrated CMOS sensors, each dedicated to green and red color imaging. To ensure that both colors are imaged in the same plane, users need to specify the brain region of interest. The LD version supports 2-color imaging at 0-3.4 mm in depth, and LV version supports 2.9-5.9 mm depths.
Additional modalities
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Combining Prism glass for “lateral” imaging
Typical miniscopes image cell populations located directly beneath their flat imaging windows (cranial widow or GRIN lens depending on the system). However, upon custom-request, all Doric microscopes can be coupled with a prism mirror to enable lateral imaging. This configuration offers two key advantages:
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Layered Imaging – Collect data from multiple layers simultaneously from a brain structure, providing a more comprehensive view of neural activity.
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Reduced Tissue Damage – The sharp edge of the prism glass minimizes tissue damage and immune response after implantation, compared to traditional blunt probes.
This prism-assisted imaging method has been successfully implemented by customers for imaging both deep and superficial brain structures.
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Microscopy Data Analysis with danse™
Finally, Doric Lenses also provides a data analysis software, danse™, for the analysis of all microscopes' data without any coding required. The danse™ software is locally installed on PC, without requiring cloud base access. The software provides a simplified interface for CaImAn, Minian and Suite2p to easily choose the right processing parameters without having to run the entire pipeline. All behavioral data including the animal tracking, speed, and movement metrics can be analyzed and aligned with microscopy data for DF/F calculation, perievent and heat maps analysis. To learn more about it check danse™ software and register for monthly webinars on danse demo here:
| Comparison Table for Doric Lenses Miniature Microscopy systems | ||||
| System Type | Deep brain 1-color |
Surface 1-color |
Deep brain 2-color |
Surface 2-color |
| Electronic focus | Yes | No | No | No |
| Optogenetic option | Yes | Yes | No | No |
| Fluid injection option | Yes | Yes | Yes | Yes |
| Rotary joint option | Yes | Yes | Yes | Yes |
External References
Deep Brain Miniscope |
| a- Using GRIN lens implantation: |
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Cortical representations of affective pain shape empathic fear in male mice. |
| Huang et al. Ventromedial prefrontal neurons represent self-states shaped by vicarious fear in male mice. Nature Communications 14, (2023) Brain region: Ventromedial prefrontal cortex (vmPFC) |
| Shin et al. Early adversity promotes binge-like eating habits by remodeling a leptin-responsive lateral hypothalamus–brainstem pathway. Nature Neuroscience 26, (2023). Brain region: Lateral Hypothalamus (LH) |
| J.N. Siemian. An excitatory lateral hypothalamic circuit orchestrating pain behaviors in mice. eLife (2021) Brain region: Lateral Hypothalamus (LH) |
| F. Fredes et al. Ventro-dorsal Hippocampal Pathway Gates Novelty-Induced Contextual Memory Formation. Current Biology 31, 25–38.e5 (2021) Brain region: Ventral hilus; dorsal dentate gyrus |
| D. Rossier et al. A neural circuit for competing approach and defense underlying prey capture. PNAS (2021) Brain region: Lateral Hypothalamus (LHA) |
| P. Krzywkowski et al. Dynamic encoding of social threat and spatial context in the hypothalamus. eLife 9, e57148 (2020) Brain region: Hypothalamus (VMHvl) |
| J.M. Patel et al. Sensory perception drives food avoidance through excitatory basal forebrain circuits. eLife 8, e44548 (2019) Brain region: basal forebrain (BF) |
| Fu et al. SatB2-Expressing Neurons in the Parabrachial Nucleus Encode Sweet Taste Cell reports 27 , 1650-1656 (2019) Brain region: parabrachial nucleus (PBN) |
| B. Roberts et al. Ensemble encoding of action speed by striatal fast-spiking interneurons Brain structure and function (2019) Brain region: dorsal striatum (DS) |
| S. Shin et al. Drd3 Signalling in the Lateral Septum Mediates Early Life Stress-Induced Social Dysfunction Neuron 97, 195–208 (2018) Brain region: lateral septum (LS) |
| E. Gallo et al. Accumbens dopamine D2 receptors increase motivation by decreasing inhibitory transmission to the ventral pallidum. Nature Communication 9, 1086 (2018) Brain region: nucleus accumbens (NAc) |
| D.A. Evans et al. A synaptic threshold mechanism for computing escape decisions Nature 558 , 590–594 (2018) Brain region: dorsal periaqueductal gray (dPAG); medial superior colliculus(mSC) |
| T.C. Francis et al., Molecular basis of dendritic atrophy and activity in stress susceptibility. Molecular psychiatry 22, 1512–1519(2017) Brain region: nucleus accumbens (NAc) |
| b- Using GRIN lens+PRISM glass implantation: |
| S. Malvaut et al. Live imaging of adult neural stem cells in freely behaving mice using mini-endoscopes Star Protocols, (2021). Brain region: Subventricular Zone (SVZ) / Lateral Ventricle (LV) |
| A. Gengatharan et al. Adult neural stem cell activation in mice is regulated by the day/night cycle and intracellular calcium dynamics. Cell 184, 709–722 (2021). Brain region: Subventricular Zone (SVZ) / Lateral Ventricle (LV) |
Surface Miniscope |
| a. Cranial Window installation: |
| A. Chenani et al., Repeated stress exposure leads to structural synaptic instability prior to disorganization of hippocampal coding and impairments in learning Transnational Psychiatry, (2022) Brain region: Hippocampus (CA1) |
| A. Glas et al. Benchmarking miniaturized microscopy against two-photon calcium imaging using single-cell orientation tuning in mouse visual cortex Plos One (2019) Brain region: visual cortex (V1) |
| b. Cranial Window+PRISM glass installation: |
| A. Glas et al. Spaced training enhances memory and prefrontal ensemble stability in mice. Current Biology (2021) Brain region: dorsomedial prefrontal cortex (dmPFC) |
| STAR Protocol |
| B.T. Laing et al. Fluorescence microendoscopy for in vivo deep-brain imaging of neuronal circuits. Journal of Neuroscience Methods, (2021). |
| S. Malvaut et al. Live imaging of adult neural stem cells in freely behaving mice using mini-endoscopes Star Protocols, (2021). Brain region: Subventricular Zone (SVZ) / Lateral Ventricle (LV) |