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In vivo Brain Circuit Analysis

The “In vivo Brain Circuit Analysis” platform is a research infrastructure devoted to integrating methods and techniques to interrogate neuronal circuits in health and disease using advanced methods for the perturbation and recording of cell activity.

If you are interested in using the platform contact:

Currently we have the following equipment available for users:

1) Equiptment fully funded by MultiPark and available to all interested users:

1.1 Inscopix nVue implantable miniature microscope system (

The Inscopix Miniature microscope system allows to image large-scale brain circuit dynamics via in vivo calcium imaging in freely behaving animals to correlate neural activity with behaviour.  nVue enables imaging of two distinct brain signals to gain deeper insight into how an ensemble of brain signals interacts during free behaviour in a single imaging session.

  • Image two distinct cellular populations from shallow or deep brain regions simultaneously with single-cell resolution
  • Explore the relationship of up to two brain signals during naturalistic behaviour
  • Record multi-channel data using nVue’s expanded data storage, facilitating longitudinal data acquisition over months

The Inscopix nVue system is basically a miniature microscope that can be attached to implanted GRIN lenses. Light, emitted by e.g. Calcium indicators, can be recorded at a single cell resolution in freely behaving animals. 

Included in the platform:

Inscopix Miniscope system 
                      - nVUE System for Dual Colour in vivo Imaging
                      - Application module (Baseplate covers, Dummy scope)
                      - Data acquisition box (DAQ)
                      - Data acquisition software
                      - Software licence 
                      - ProView Implant Kit (Lens holding device, stereotax rod, screw adjustment tool)
                      - Inscopix care (free repairs, overnight shipping on ALL components)

Services provided:
(i) advise on planning of experiments
(ii) introduction to hardware
(iii) introduction to analysis software
(iv) management of booking
(v) maintaining equipment

Experimental costs such as lenses, AAV vectors, research animals, etc will be solely carried by the experimenter. 

Some AAV vectors might be available for testing (e.g. leftover stock).

Schematics of the included apparatuses in the research infrastructure.
Data Acquisition Box connected to the microscope. Schematic of rodent brain depicting the deposition of the Calcium indicator via stereotaxic injection. Schematic of implantable GRIN lens. Schematic of rodent brain with the GRIN lens implanted above the area of Calcium indicator injection.


2) Equipment that can be accessed but is NOT owned by MultiPark:
(Note that access to these are under agreement with the respective group).

2.1 Lasers for optogenetic stimulation (BNL)
Contact: andreas [dot] heuer [at] med [dot] lu [dot] se

We have a blue and a yellow laser including a M.A.S.T.E.R. 8 controller for optogenetic stimulation. The setup is movable and has been used with our operant boxes, freely moving recordings, electrochemistry in vivo and cell culture electrochemistry recordings. 

  • 50mW 589 (yellow)
  • 50mW 473 (blue)
  • 150mW 473 (blue)
  • TTL pulse generator
  • M.A.S.T.E.R.8 controller
  • Patch Cable (50um or 200um Core)
  • Protective eyewear
  • Light power meter (Thorlabs)
Picture of laser generator. Optrode emitting yellow or blue light. Labelled rat midbrain section.
DPSSL driver with MGL-III-473-50mW laser generator. Optrode emitting yellow (top) or blue (bottom) light. Rat midbrain section labelled immunohistochemically for dopaminergic neurons (TH, Magenta) and Channelrhodopsin 2 (ChR2-GFP, green).

Doric FP 

2.2 Amperometry (Chronoamperometry and Constant potential amperometry) BNL
Contact: andreas [dot] heuer [at] med [dot] lu [dot] se (andreas[dot]heuer[at]med[dot]lu[dot]se)

We us carbon fibre electrodes and/or microelectrode arrays to measure analytes of interest in vitro and in vivo. We have set up electrochemical detection for Dopamine, Glutamate, and GABA. Additional neurotransmitter systems that can be analysed but have not been used by our laboratory can be found here.  Electrochemistry allows for the sub-second recordings of neurotransmitters in acute and chronic recordings. Our system is fully optogenetics compatible and we can perform recordings in vitro, anaesthetised, and freely moving rodents. 

Picture of the F.A.S.T. system (Quanteon) for electrochemical recordings and graphs of results.
F.A.S.T. system (Quanteon) for electrochemical recordings with headstage amplifier. Schematic of self-referencing principle used with Micro Electrode Arrays (MEA). Electrochemical trace of optogenetically evoked dopamine release. Screenshot of glutamate recordings in prefrontal cortex.

2.3 Recording setup for pose estimation in rodents (rats and mice) BNL

Pose estimation enables the marker free tracking of animals in 3 dimensions over time. It is based on computer vision and transfer learning utilizing deep neural networks. 

A good way to start are the DeepLabCut implementation ( and the AI/ML knowledge base from MultiPark (; par [dot] halje [at] med [dot] lu [dot] se)

  • 6 camera setup for parallel video recordings (1920x1200; 1920x1080; 1280x720)
  • ML algorithms for the tracking of rodents (rats and mice) of >30 body parts
  • Optogenetics/Ca-imaging compatible (through rotary joints/commutators)
Photograph of recording frame for rats and screenshots of rats in recording chambers.
Photograph of recording frame for rats. Screenshot of pose estimation in rats (top) and movement of body parts (tail: red; nose: purple) in 2D space. Photograph of rat in the cylinder (top) and rendered skeleton (bottom).

2.4 Rat operant chambers (8x) (modular: 2 retractable levers; 9-hole response array) BNL
Contact: andreas [dot] heuer [at] med [dot] lu [dot] se (andreas[dot]heuer[at]med[dot]lu[dot]se)

Operant chambers allow to study animal behaviour in a computer controlled environment. We have established takss by teaching an animal to perform certain actions (e.g. pressing a lever or poking into a response hole) in response to a specific stimuli (e.g. tone or light). Many tasks tap into motor and non-motor domains (cognitive and psychiatric= 

We have the following paradigms established:

- Lateralised choice reaction time task (attention, lateralised neglect, reaction times, movement times)
- 5 choice serial reaction time task (attention, reaction time)
- Progressive ratio (motivation)
- Delayed alternation (Short term memory)
- Delayed (non-) matching to position (short term memory)

Photographs of modular operant chambers.
Photograph of modular operant chambers. Photograph of operant chamber from the inside. Photograph of rat performing the 5-choice serial reaction time task.

2.5 ML based quantification of cells (BNL)

We have trained networks to detect and quantify cells from microscope images. Currently we have the following cell types available: Microglia (Iba1, Ox42/cd11b); Dopamine cells (TH).

Our algorithms are performing best on DAB stained tissue but can be adapted to other immunolabeled tissue. 

Although analysis is possible on any computer, we have a powerful GPU setup which enables a much faster processing time. 

2.5.1 ML based quantification of Microglial cells (DAB staining)

2.5.2 ML based quantification of TH-ir cells (DAB staining)

2.5.3 Fiji-macro for quantification of axonal swellings
doi: 10.1016/j.jneumeth.2022.109640

Photograph of rat substantia nigra analyzed with our ML algorithm for the detection of DAB immunolabeled cells (TH).
Photograph of rat substantia nigra analysed with our ML algorithm for the detection of DAB immunolabeled cells (TH). High magnification indicating the detected cells (orange circle). Photograph of DAB stained sections immunolabelled for microglia (Iba1). Photograph displaying the detected microglia cells indicated by bounding boxes including the probability.



Andreas Heuer

Senior lecturer
E-mail: andreas [dot] heuer [at] med [dot] lu [dot] se (andreas[dot]heuer[at]med[dot]lu[dot]se)
Phone: +46 70 883 62 98