Amendment_00001_8-15-19.pdf

SF-30 CONTINUATION SHEET 00001 Page 2 of 14

A. Answers to Questions

1. Question: We would like to know what is mean by integration of the 3 components in the software. From the solicitation:

“Tight integration between microscope, micromanipulators, and stage is required for the complex experiments planned for the LCSMS. The Contractor must provide a software package that allows users, through a graphical user interface (GUI), to control all three and coordinate their movement for the sake of multipatch recording. The software package must be compatible with the Windows 10 (64 bit) operating system.”

Is there a requirement for the manipulators to be controlled via software and, if so, in what way? Typically these are controlled by hand with a motorized hand wheel by the researcher.

Answer: The NINDS LCSMS requires fully integrated software control of electrophysiology experiments. Please refer to the revised Purchase Description in Track Changes for further clarification.

(End of Answers to Questions)

B. Summary of Changes to the Solicitation

1. The Purchase Description is replaced in its entirety and incorporated as follows.

NIH‐NINDS‐75N95019Q00246 Amendment 00001 08/15/2019

PURCHASE DESCRIPTION

1. Statement of Need and Purpose

The National Institute of Neurological Disorders and Stroke (NINDS) is establishing a new laboratory that will use cutting-edge physiological, imaging, and behavioral methods to investigate the relationship between human neurological disorders and brain function at the molecular, synaptic, cellular, and circuit levels. The new laboratory requires several systems, including complete rigs for brain slice electrophysiology and multiphoton imaging (both in vitro and in vivo). Given the complexity of the planned experiments, systems that integrate tightly with each other are required.

2. Background Information and Objective

The LCSMS will study fundamental issues of synaptic transmission, neuronal excitability, neuromodulation, and neural circuit activity using animal models (principally, the mouse).

These issues will be related to human neurological disorders, such as Alzheimer’s and other neurodegenerative disorders, and will be explored in brain areas including (but not limited

to) the amygdala, basal forebrain cholinergic areas, the ventral hippocampus, and the prefrontal cortex.

3. Generic Name of Product

Electrophysiology and multiphoton imaging rigs

4. Salient Characteristics

A major line of research will employ patch clamp electrophysiology, multiphoton imaging, and virtual reality. This research requires four systems that must be tightly integrated with each other: (1) a rig capable of multipatch recording from cell bodies and dendritic structures in brain slices, imaging of fluorescently-tagged neurons and dendrites, and simultaneous widefield photoactivation (i.e., optogenetic stimulation or neurotransmitter uncaging); (2) a rig with these same capabilities plus laser-based components for focal and patterned photoactivation; (3) a rig capable of simultaneous multiphoton microscopy, photoactivation, and multipatch recording in brain slices; and (4) a rig capable of simultaneous multiphoton microscopy and photoactivation that can be used with an awake, head-fixed mouse walking on a treadmill or floating ball and that can accommodate a virtual reality environment made up of several large thin-film-transistor (TFT) liquid crystal displays.

The four systems shall be tightly integrated with each other and allow for components to be swapped between them for maximum flexibility in experimental design. The need for integration and component swapping is explained further in the last part of the Salient Characteristics section.

These four complete electrophysiology and/or multiphoton imaging systems shall have the capabilities (salient characteristics) listed in the following table where Y = Yes and N = No.

Rig 1 Rig 2 Rig 3 Rig 4

Brain slice electrophysiology

Y Y Y N

LED optogenetic stimulation

Y Y N N

Laser optogenetic stimulation

N Y Y Y

Multiphoton imaging on brain slices

N N Y N

Multiphoton imaging with awake mice

N N N Y

Used in conjunction with virtual reality

N N N Y

The four systems are specified in more detail in the next four subsections. A description of the need for integration and component swapping between the systems immediately follows.

RIG 1: PATCH CLAMP ELECTROPHYSIOLOGY

One patch clamp electrophysiology system with tight, computer-controlled integration between the microscope, stage, and manipulator elements.

Include at least four micromanipulators capable of patch clamp recording from structures as small as the dendrites of mouse neocortical neurons. The micromanipulators must have a travel distance in every direction of at least 20 mm, a spatial resolution of 20 nm, and a drift of no more than 1 micron over two hours. It should be possible to expand the number of micromanipulators to six, with independent pipette exchange on all six. It should be possible to transform micromanipulators from a right-hand configuration to a left-hand configuration. It should be possible to link movement along the X and Z axes so that electrodes move diagonally along a virtual 4th axis at a user-specified angle.

An upright microscope equipped with infrared-differential interference contrast (IR- DIC) optics (for visualized patch recording in brain slices as thick as 400 microns) and epifluorescence equipment (for all widely-used fluorophores, including GFP, mCherry, tdTomato). The microscope should have motorized condenser and objective arms to allow for remote control, including through computer software. Must include 4x and 40x objectives.

A motorized XY stage that can be controlled by computer software.

Tight integration between microscope, micromanipulators, and stage is required for the complex experiments planned for the LCSMS. The Contractor must provide a software package that allows users, through a graphical user interface (GUI), to control all three and coordinate their movement for the sake of multipatch recording. The software package must be compatible with the Windows 10 (64 bit) operating system.

A CCD camera suitable for both IR-DIC (visualized patch) and fluorescence

(identification of fluorescently-tagged structures) imaging. A frame rate of at least 20 fps and at least 14-bit resolution are required. The camera should connect to a computer via a USB 3.0 interface and include imaging software.

A platform and chamber for brain slices.

A low-noise temperature controller for bath salines.

A perfusion pump for bath salines.

package that allows users, through a graphical user interface (GUI), to control all three and coordinate their movement for the sake of multipatch recording. The software package should also be capable of integrating information from other parts of the rig (e.g., the perfusion system and the temperature controller). The software package must be compatible with the Windows 10 (64 bit) operating system. Specific requirements for the software include but are not limited to:

(a) Moving all manipulators together as a unit.

(b) When the researcher moves to a different field of view in a brain slice, the manipulators shall have to ability to follow along.

(c) Leave one manipulator at a given position and then move the field of view (along with the other manipulators) to a different place in the brain slice.

(d) The software shall keep track of the positions of all motorized units and be able to return to stored positions or move to user-specified positions.

(e) Read the approach angles of manipulators.

(f) Store and implement user preferences, such as speed/acceleration and direction of movement, step sizes, and memory positions.

(g) Provide visual displays of positional information.

(h) Provide GUI controls (e.g., virtual joysticks) to facilitate manipulator control through software.

(i) Control multiple motorized units (10+) simultaneously.

An anti-vibration table with Faraday cage. The table must be no larger than 30 inches by 36 inches.

Patch clamp amplifiers suitable for both current clamp and voltage clamp recordings.

At least four channels of amplification must be available. The amplifiers must have built-in circuitry for standard electrophysiological compensation modes (e.g., bridge balance, fast and slow pipette capacitance compensation, series resistance compensation). The amplifiers must be computer-controlled and should interface with open-source electrophysiology software written in a widely-used language such as Matlab, LabView, or Python. Matlab is the preferred language.

RIG 2: PATCH CLAMP ELECTROPHYSIOLOGY (WITH LASER STIMULATION)

One patch clamp electrophysiology system with tight, computer-controlled integration between the microscope, stage, and manipulator elements. This system must include a laser-based subsystem for focal and patterned optogenetic stimulation.

micromanipulators must have a travel distance in every direction of at least 20 mm, a spatial resolution of 20 nm, and a drift of no more than 1 micron over two hours. It should be possible to expand the number of micromanipulators to six, with independent pipette exchange on all six. It should be possible to transform micromanipulators from a right-hand configuration to a left-hand configuration. It should be possible to link movement along the X and Z axes so that electrodes move diagonally along a virtual 4th axis at a user-specified angle.

An upright microscope equipped with infrared-differential interference contrast (IR- DIC) optics (for visualized patch recording in brain slices as thick as 400 microns) and epifluorescence equipment (for all widely-used fluorophores, including GFP, mCherry, tdTomato). The microscope should have motorized condenser and objective arms to allow for remote control, including through computer software. Must include 4x and 40x objectives.

A motorized XY stage that can be controlled by computer software.

package that allows users, through a graphical user interface (GUI), to control all three and coordinate their movement for the sake of multipatch recording. The software package must be compatible with the Windows 10 (64 bit) operating system.

A CCD camera suitable for both IR-DIC (visualized patch) and fluorescence

(identification of fluorescently-tagged structures) imaging. A frame rate of at least 20 fps and at least 14-bit resolution are required. The camera should connect to a computer via a USB 3.0 interface and include imaging software.

package that allows users, through a graphical user interface (GUI), to control all three and coordinate their movement for the sake of multipatch recording. The software package should also be capable of integrating information from other parts of the rig (e.g., the perfusion system and the temperature controller). The software package must be compatible with the Windows 10 (64 bit) operating system. Specific requirements for the software include but are not limited to:

(a) Moving all manipulators together as a unit.

(b) When the researcher moves to a different field of view in a brain slice, the manipulators shall have to ability to follow along.

(c) Leave one manipulator at a given position and then move the field of view (along with the other manipulators) to a different place in the brain slice.

(d) The software shall keep track of the positions of all motorized units and be able to return to stored positions or move to user-specified positions.

(e) Read the approach angles of manipulators.

(f) Store and implement user preferences, such as speed/acceleration and direction of movement, step sizes, and memory positions.

(g) Provide visual displays of positional information.

(h) Provide GUI controls (e.g., virtual joysticks) to facilitate manipulator control

An anti-vibration table with Faraday cage. The table must be no larger than 36 inches by 48 inches.

Patch clamp amplifiers suitable for both current clamp and voltage clamp recordings.

At least four channels of amplification must be available. The amplifiers must have built-in circuitry for standard electrophysiological compensation modes (e.g., bridge balance, fast and slow pipette capacitance compensation, series resistance compensation). The amplifiers must be computer-controlled and should interface with open-source electrophysiology software written in a widely-used language such as Matlab, LabView, or Python. Matlab is the preferred language.

Include components for laser-based optogenetic stimulation or neurotransmitter uncaging. The components must include a galvanometer-based method for quickly and reliably positioning the laser beam. A software package must be provided allowing users to determine stimulation pattern and settings using a GUI. The components must allow for stimulation/uncaging at commonly-used wavelengths – namely, those for channelrhodpsin, halorhodopsin, and caged glutamate.

RIG 3: MULTIPHOTON IMAGING ON BRAIN SLICES

One system capable of simultaneously performing and integrating three functions: (A) multiphoton imaging, (B) optogenetic stimulation or neurotransmitter uncaging (i.e., photoactivation), and (C) patch clamp electrophysiology from multiple neuronal structures within brain slices.

The system will be installed, together with a second multiphoton system, on a 5’ x 10’ anti-vibration table in Building 35A. The table will be in a room formed by combining the present rooms 3B-415 and 3B-214; the new room will have the dimensions 14 feet 4 ¾ inches x 15 feet 7 inches. The table will also house two lasers, which together with associated optical components, will take up approximately 20 square feet of table space and a virtual reality system, which will take up 10 square feet of table space. There will be an equipment cage (approximately 3’ x 8’) mounted above the air table. The room will be devoted to these two multiphoton systems. Given these table/room characteristics: the following size limitations apply to Rig 3: (1) the system should require no more than 10 square feet of anti-vibration table space; (2) the system should require no more than 12 square feet of the overhead cage space; and (3) all other associated electronics should fit in a relay rack no wider than 26” and no taller than 8’. Both Rig 3 and Rig 4 (described below), including all associated lasers and electronic/optical components, must fit in the designated room.

(A) Multiphoton Imaging

The microscope must be able to manipulate two light paths in order to make possible simultaneous two-photon imaging and photoactivation.

The system must allow users to choose between these scanning configurations for the imaging path: galvo/galvo, resonant/galvo, and resonant/galvo/galvo.

The lenses of the scanhead must allow transmission between 700 nm and 1400 nm.

The system must have some means of reducing sound noise (to below 20 dB SPL at a distance of 5’). Although the system will be used with brain slices, the room in which it will be housed will also host experiments on awake behaving mice. Minimizing sound is crucial.

Scanning in the Z direction should have a minimum step size no larger than 0.1 microns.

The system will share two tunable lasers with a second multiphoton system installed on the same anti-vibration table. Systems that cannot do this are not acceptable.

The system should therefore be compatible with Matlab-based control software, such as

ScanImage (Janelia).

The multiphoton microscope will be used immediately for experiments on brain slices, but the LCSMS may decide at some point to modify it for use with awake, head-fixed mice. It should be possible to simply convert the multiphoton microscope to an in vivo configuration.

(B) Photoactivation

The system will be used for simultaneous two-photon imaging and photoactivation (i.e., optogenetic stimulation or neurotransmitter uncaging). The system should therefore be able to manipulate a second laser beam for this purpose.

Software – ideally, Matlab-based – must be provided for this purpose. This software must allow users to determine scanning pattern using a graphical user interface (GUI).

Arbitrary patterns of stimulation (e.g., spirals, zig-zags, squares, arbitrary shapes) must be possible through the provided software.

(C) Electrophysiology micromanipulators must have a travel distance in every direction of at least 20 mm, a spatial resolution of 20 nm, and a drift of no more than 1 micron over two hours. It should be possible to easily transform micromanipulators from a right-hand configuration to a left-hand configuration. It should be possible to link movement along the X and Z axes so that electrodes move diagonally along a virtual 4th axis at a user-specified angle.

Tight integration between microscope and micromanipulators is required for the complex experiments planned for the LCSMS. The Contractor must provide a software package that allows users, through a graphical user interface (GUI), to control all them and coordinate their movement for the sake of multipatch recording. The software package must be compatible with the Windows 10 (64 bit) operating system.

package that allows users, through a graphical user interface (GUI), to control all three and coordinate their movement for the sake of multipatch recording. The software package should also be capable of integrating information from other parts of the rig (e.g., the perfusion system and the temperature controller). The software package must be compatible with the Windows 10 (64 bit) operating system. Specific requirements for the software include but are not limited to:

(a) Moving all manipulators together as a unit.

(b) When the researcher moves to a different field of view in a brain slice, the manipulators shall have the ability to follow along.

(c) Leave one manipulator at a given position and then move the field of view (along with the other manipulators) to a different place in the brain slice.

(d) The software shall keep track of the positions of all motorized units and be able to return to stored positions or move to user-specified positions.

(e) Read the approach angles of manipulators.

(f) Store and implement user preferences, such as speed/acceleration and direction of movement, step sizes, and memory positions.

(g) Provide visual displays of positional information.

(h) Provide GUI controls (e.g., virtual joysticks) to facilitate manipulator control

Patch clamp amplifiers suitable for both current clamp and voltage clamp recordings. At least four channels of amplification must be available. The amplifiers must have built-in circuitry for standard electrophysiological compensation modes (e.g., bridge balance, fast and slow pipette capacitance compensation, series resistance compensation). The amplifiers must be computer-controlled and should interface with open-source electrophysiology software written in Matlab.

RIG 4: MULTIPHOTON IMAGING WITH AWAKE MICE

One system capable of simultaneously performing and integrating two functions: (A) multiphoton imaging and (B) optogenetic stimulation or neurotransmitter uncaging (i.e., photoactivation). The system will be used to study neural circuits in a head-fixed but awake mouse sitting on a floating spherical ball or a treadmill and navigating through a virtual reality space (created by large video displays in the mouse’s field of view). (C) The microscope must be able to accommodate both the ball/treadmill and the virtual reality displays.

The system will be installed, together with a second multiphoton system, on a 5’ x 10’ anti-vibration table in Building 35A. The table will be in a room formed by combining the present rooms 3B-415 and 3B-214; the new room will have the dimensions 14 feet 4 ¾ inches x 15 feet 7 inches. The table will also house two lasers, which together with associated optical components, will take up approximately 20 square feet of space and a virtual reality system, which will take up 10 square feet of space. There will be an equipment cage (approximately 3’ x 8’) mounted above the air table. The room will be devoted to these two multiphoton systems. Given these table/room characteristics: the following size limitations apply to Rig 4: (1) the system should require no more than 10 square feet of anti-vibration table space;

(2) the system should require no more than 12 square feet of the overhead cage space; and

(3) all other associated electronics should fit in a relay rack no wider than 26” and no taller than 8’. Both Rig 3 (described above) and Rig 4, including all associated lasers and electronic/optical components, must fit in the designated room.

(A) Multiphoton Imaging

The microscope must be able to manipulate two light paths in order to make possible simultaneous two-photon imaging and photoactivation.

The system must allow users to choose between these scanning configurations for the imaging path: galvo/galvo, resonant/galvo, and resonant/galvo/galvo.

The lenses of the scanhead must allow transmission between 700 nm and 1400 nm.

The system will be used with awake behaving mice and must have some means of reducing sound noise (to below 20 dB SPL). Minimizing sound is crucial.

Scanning in the Z direction should have a minimum step size no larger than 0.1 microns.

The system will share two tunable lasers with a second multiphoton system installed on the same anti-vibration table. Systems that cannot do this are not acceptable.

The system should therefore be compatible with Matlab-based control software, such as

ScanImage (Janelia).

The multiphoton microscope will be used immediately for experiments on awake mice, but the LCSMS may decide at some point to modify it for use on brain slices. It should be possible to simply convert the multiphoton microscope to an in vitro configuration.

(B) Photoactivation

The system will be used for simultaneous two-photon imaging and photoactivation (i.e., optogenetic stimulation or neurotransmitter uncaging). The system should therefore be able to manipulate a second laser beam for this purpose.

Software – ideally, Matlab-based – must be provided for this purpose. This software must allow users to determine scanning pattern using a graphical user interface (GUI).

Arbitrary patterns of stimulation (e.g., spirals, zig-zags, squares, arbitrary shapes) must be possible through the provided software.

(C) Virtual Reality

In this document, the term “virtual reality” refers to systems that use interactive, computer-generated manipulations of sensory experience to create brain states or provoke behavioral responses mimicking those corresponding to the physical environments being simulated on the computer. A broad review of contemporary efforts is given by Thurley and Ayaz, Curr. Zool. 63:109-119 (2017). For the planned experiments of the LCSMS, the virtual reality environment will be created by 6 liquid crystal displays (approximately 19” diagonal and 17” height) arranged so that each display is approximately 15" from the microscope’s light path and the displays together wrap around to encompass 270⁰ of the view in the XY plane.

To accommodate a “mouse-sized” spherical running ball, the minimum distance between the bottom of the objective and the anti-vibration table must be no smaller than

10 inches. Likewise, it should be possible to extend the distance between the light path and the microscope frame to at least 8 inches.

In some cases, it would be useful to tilt the objective away from the vertical axis in order to image more lateral parts of the mouse brain. The microscope should accommodate this need.

The system will be used in conjunction with a virtual reality system consisting of several video displays. (A prominent commercial example is the Virtual Reality JetBall built by Phenosys and distributed in North America by Blackrock Microsystems.) The microscope system must be compatible with such virtual reality equipment.

INTEGRATION AND COMPONENT SWAPPING

In each of the four cases (Rigs 1-4), a complete system is desired because of the complexity of the planned experiments. It is imperative that every piece of equipment (manipulators, microscope, XY stage, lasers, LEDs, amplifiers) works well with all the other parts. It is also very important that a unified software package be available to aid in this integration.

The four systems are presented together in a single purchase description because they must be integrated together in terms of (A) hardware and (B) user experience (especially software) and (C) because the LCSMS wishes to maximize flexibility in its experimental planning by allowing components to be swapped from one rig to another.

INTEGRATION (hardware)

Rigs 3 and 4 will share two tunable lasers. One laser will provide the laser beam for multiphoton imaging while the other laser will provide the laser beam for optogenetic stimulation. This will be true – simultaneously – for both rigs. For laser sharing to work, the two rigs must be tightly integrated with each other, both to accommodate the two lasers and to coordinate their use.

INTEGRATION (user experience) Members of the LCSMS may be required, depending on scientific need, to switch between various types of experiments: in vitro physiology, in vitro physiology with laser stimulation, in vitro physiology with multiphoton imaging, multiphoton imaging in vivo. For such switching to work seamlessly, the rigs must contain compatible hardware (particularly the manipulators) and be run by the same software (at present, the LCSMS anticipates a complete Matlab-based suite of software).

COMPONENT-SWAPPING

The four rigs have overlapping capabilities. Depending upon future experimental needs, the LCSMS might wish swap equipment between the four rigs. To cite one example, the LCSMS may wish to transfer two micromanipulators and one amplifier from one patch clamp rig to a different patch clamp rig to allow the second rig to be capable of six simultaneous patch recordings. To cite another, the LCSMS may wish to move a treadmill from the in vivo multiphoton rig (Rig 4) to the in vitro multiphoton rig (Rig 3) to convert the latter to in vivo use. Such flexibility requires the hardware to be compatible and (ideally) interchangeable.

5. Quantity

Four (4) systems

6. Delivery Date

The Contractor shall deliver and install the equipment within 90 days after receipt of order.

Delivery must be Freight on Board (FOB) Destination and include inside delivery. On-site training must take place within two (2) weeks of equipment installation. The equipment shall be delivered and installed in coordination with the Contracting Officer’s Representative (COR). The contractor shall provide an Original Equipment Manufacturer (OEM) certified service technician to perform setup, installation, and an on-site 2-day training session for staff members.

7. Warranty

The Contractor shall warrant that the Equipment will be free from defects for a period of twenty-four (24) months from the date of installation, inspection by the Government and acceptance.

8. Delivery Requirements

The Contractor shall deliver and install the required equipment in coordination with the COR.

Delivery must be FOB Destination and must include inside installation. This system will be delivered to newly renovated space in building 35A. Coordination of delivery will be performed with the COR at the time the equipment is ready to be shipped. The equipment shall be delivered and installed between the hours of 8:00am and 5:00pm, Bethesda, MD local prevailing time, Monday through Friday. This system will be delivered to newly renovated space in building 35A. Coordination of delivery will be performed with the Government at the time the equipment is ready to be shipped.

Laboratory of Circuits, Synapses, and Molecular Signaling (LCSMS) National Institute of Neurological Disorders and Stroke Bldg 35A/ Rm GF301 35A Convent Dr Bethesda, MD 20892

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(End of Summary of Changes to the Solicitation)