SOLICITATION NOTICE
66 -- Upgrade of Neurolucida Microscope Imaging Software
- Notice Date
- 8/22/2014
- Notice Type
- Presolicitation
- NAICS
- 511210
— Software Publishers
- Contracting Office
- Department of Health and Human Services, National Institutes of Health, National Institute on Drug Abuse, Station Support/Simplified Acquisitions, 31 Center Drive, Room 1B59, Bethesda, Maryland, 20892
- ZIP Code
- 20892
- Solicitation Number
- HHS-NIH-NIDA-SSSA-NOI-14-637
- Archive Date
- 9/23/2014
- Point of Contact
- Megan Ault,
- E-Mail Address
-
megan.ault@nih.gov
(megan.ault@nih.gov)
- Small Business Set-Aside
- N/A
- Description
- INTRODUCTION This is a pre-solicitation non-competitive (notice of intent) synopsis to award a contract without providing for full or open competition (including brand-name). THIS IS A NOTICE OF INTENT, NOT A REQUEST FOR PROPOSAL. A SOLICITATION WILL NOT BE ISSUED AND PROPOSALS WILL NOT BE REQUESTED. The National Institute on Drug Abuse (NIDA), Consolidated Station Support and Simplified Acquisitions (CSS/SA) Branch intends to negotiate and award a purchase order to MBF Biosciense for an upgrade of Neurolucida microscope imaging software without providing for full and open competition (including brand-name). NORTH AMERICAN INDUSTRY CLASSIFICATION SYSTEM (NAICS) CODE The intended procurement is classified under NAICS code 511210 with a Size Standard of $38.5 million. REGULATORY AUTHORITY The resultant contract will include all applicable provisions and clauses in effect through the Federal Acquisition Circular (FAC) 05-72 dated January 30,2014. This acquisition is for a commercial item or service and is conducted under the procedures as prescribed in FAR subpart 13-Simplified Acquisition Procedures. This acquisition is NOT expected to exceed the simplified acquisition threshold. STATUTORY AUTHORITY This acquisition is conducted under the authority of the authority of FAR Subpart 13.106-1. DESCRIPTION OF REQUIREMENT Purpose and Objectives The purpose of this requirement is the acquisition of an upgrade of the Neurolucida software to incorporate functions that will enhance image acquisition of brain sections, their assembly into full three-dimensional reconstructions and analysis of brain circuits by the National Institute of Mental Health (NIMH) Section on Neuroanatomy, Laboratory of Systems Neuroscience, DIRP. Period of Performance Delivery shall be approximately three (3) months after receipt of award. A firm fixed price purchase order is contemplated. Project Description The following is the current process used in the Section on Neuroanatomy to produce a fully reconstructed imaged mouse brain with labeling of select neurons in a specific brain region such as the cerebral cortex and their axonal projections throughout the brain, including the brain stem: 1) Histology: Coronal brain sections (50 µm) are processed histologically with up to four fluorescent labels. Sections are mounted onto 10 microscope slides (12-15 sections/slide). A full mouse brain consists of 120-150 sections. 2) Image Acquisition (Neurolucida): Each slide with 12 sections is imaged using Neurolucida software on Zeiss microscope with motor driven stage. For one slide 800 image "tiles" are acquired. Each "tile" consists of: a) Separate "channels" for each fluorophore b) Multiple "sub-channels" for a single fluorphore to accommodate full dynamic range of label (injected neurons saturate at exposures to image fine 1 µm axon processes) c) 10 focal planes at 5µm steps 3) Image Processing: The 800 tiles are compiled into a single image of 12 brain sections and then the individual sections are identified and saved as separate files. Each of these "section" files are processed as follows: a) Multiple channels for each fluorphore are "combined" to obtain single channel with fully "dynamic range" of labeling b) The channel containing the cell stain, which labels all neurons in all sections, is normalized to "flatten" staining c) Labeling of specific neurons and processes is separated from background and artifact staining d) 10 focal planes are reduced to one using "deep focus" image algorithm to produce single image plane for each section with labeled neurons and processes focally optimal 4) Assembly of brain sections into fully reconstructed brain: a) Brain sections are put into sequence order. The histologic process used does not automatically order the brain sections. b) Sections are aligned to each other using algorithms involving rotation and translation using external boundary mask c) Sections are further aligned using internal landmarks d) Image files for each section are cropped to identical size e) Image files are converted into a 3-dimensional image 5) Image storage and access (Biolucida). a) Brain image files are stored in online Biolucida Database b) Image files are organized using "tagging" feature c) Online access allows presentation of data and collaborations 6) Neuronal circuit analysis (Neurolucida360). The purpose of producing fully reconstructed brain image data is to analyze the organization of the circuits of the cerebral cortex and their relationship to subcortical brain structures. To conduct such studies requires the following analytic functions to be applied to the data: a) Align brains to each other using transformation and translation algorithms of features within sections that align areas within a section to the same area in another brain with offsets in 3 axes. b) Align brains to a reference atlas c) Generate contour labeling of structures within a brain, such as brain regions, nuclei, and fiber tracts d) Align contours between brains and to reference atlas e) Tools to identify and mark neuron features, including cell bodies, dendrites, spines, axons and terminal varicosities f) Provide statistical methods for analyzing marked brain features in common atlas brain space The work flow above represents our current process. Processes listed in 2) and 5) are currently done using existing MBF Bioscience Software. Processes listed in 3),4) and 5) currently require exporting image files out of the Neurolucida software platform into multiple other image software platforms including ImageJ (FIJI) and Adobe Photoshop. This adds considerable time to the work required for each brain imaged (approximately 6-8 hours per brain) due to both the time required for transfer of large image stacks and the suboptimal processing provided by these other platforms. The Scope of Work for this purchase request is to incorporate processes 3,4 and 5 into the Neurolucida platform. We have 2 microscope imaging systems and 2 workstations using Neurolucida software. The imaging systems have been specifically configured to interface the cameras (Hamamtsu Flash 4.0), motor driven stages (Ludl Instruments), fluorescence LED illumination system and Zeiss microscope with apotome and Z-axis motors (Zeiss) with Neurolucida software for image acquisition. The purchase order is for MBF Bioscience to provide additional functionality listed below. Software programming for HDR image acquisition Imaging the brain sections that contain both intensely labeled neurons and very fine processes of those neurons requires a very wide dynamic range of luminosity. Although the Hamamatsu Flash 4.0 camera (cost $25,000) used in our system has a wider dynamic range than most cameras it is not sufficient to capture the morphologic details of the labeled neurons and processes in our tissue sections. We therefore use multiple exposures of each tile for a single fluorophore (Step 2b) and blend these together in the image processing stage (Step 3a). Because this process is applied to each of the 8000 image tiles per brain at multiple steps in the imaging pipeline there is a resulting increase in both time (approximately 2 hours of processing time per brain) and image storage space while not providing an optimal solution to the problem of they luminosity dynamic range of the image. MBF Bioscience programmers will develop a process to produce the necessary luminosity HDR during the acquisition of the image and integrate that process into our existing Neurolucida software programs that control our microscope image acquisition. Software programming to incorporate image processing functions to assemble brain sections into fully reconstructed brain image In our current imaging pipeline, following acquisition of the brain sections in Neurolucida software, images are exported into ImageJ (FIJI) image program to carry out Steps 3b,c,d and 4a,b,c,d. These steps assemble the acquired image into a full three dimensional image. Functions required include: •Image processing math algorithms including those for smoothing, edge detection, Gaussian filters •Ability to combine image channels with basis image math algorithms •Spatial transformation of images including rotation and 2 and 3 dimensional translation •Image tools for selecting and modifying regions of interest MBF Bioscience programmers will incorporate these image processing functions into a customized version of Neurolucida. Software programming to provide neuronal circuit analysis functions into Neurolucida 360 Neurolucida 360 is an MBF Bioscience software package that provides tools for quantitative analysis of neurons and their dendritic and axonal processes. The fully reconstructed brains produced with Neurolucida may be analyzed in this program. For the purpose of analysis of the organization of the circuits of the cerebral cortex and their relationship to subcortical brain structures additional functions will be required. These functions are to include: a) Alignment of brains to each other using transformation and translation algorithms of features within sections that align areas within a section to the same area in another brain with offsets in 3 axes. b) Alignment of brains to a reference atlas c) Generate contour labeling of structures within a brain, such as brain regions, nuclei, and fiber tracts d) Align contours between brains and to reference atlas e) Tools to identify and mark neuron features, including cell bodies, dendrites, spines, axons and terminal varicosities f) Provide statistical methods for analyzing marked brain features in common atlas brain space Neurolucida 360 software Licenses for 3 workstations Biolucida annual renewal and server space Published data and ongoing research data are stored and accessed through Biolucida software, which is hosted by MBF Biosciences. The current purchase request provides an annual extension including the Annual license fee for Biolucida and Server storage fee for up to 1 TB of data. CONTRACTING WITHOUT PROVIDING FOR FULL OR OPEN COMPETITION (INCLUDING BRAND-NAME) DETERMINATION The determination by the Government to award a contract without providing for full and open competition is based upon the market research conducted. Laboratory of Systems Neuroscience has used Microbrightfield Bioscience (MBF Bioscience) software for over 10 years on microscope systems used in neuroanatomical studies of the organization of the mouse brain. Studies involve injections of AAV-Cre dependent viruses into targetted brain sites to drive expression of fluorescent proteins, which are used to visualize specific neuron subtypes and their axonal projections throughout the brain. Over the past 5 years NIMH has used MBF Bioscience Neurolucida software interfaced with Zeiss Microscopes and motor driven stages to develop the ability to image through every section of the mouse brains to provide a systems level analysis of neural circuit organization. The Neurolucida software interfaces with the camera, microscope and stage drive to acquire multiple fluorescent images at high resolution in a grid matrix that is assembled to provide a "seamless" montage image. The software system currently used is proprietary to MBF Bioscience. MBF is the only vendor that can provide the required added functions. Also, MBF has adapted the Neurolucida software for NIMH in the past and has delivered those added software functions in a satisfactory manner. The intended source is: Microbrightfield, Inc. 185 Allen Broon Ste 101 Williston, VT 05495-9209 CLOSING STATEMENT THIS SYNOPSIS IS NOT A REQUEST FOR COMPETITIVE PROPOSALS. However, interested parties may identify their interest and capability to respond to this notice. Responses to this notice shall contain sufficient information to establish the interested parties' bona-fide capabilities for fulfilling the requirement and include: unit price, list price, shipping and handling costs, the delivery period after contract award, the prompt payment discount terms, the F.O.B. Point (Destination or Origin), the Dun & Bradstreet Number (DUNS), the Taxpayer Identification Number (TIN), and the certification of business size. All offerors must have an active registration in the System for Award Management (SAM) www.sam.gov." A determination by the Government not to compete this proposed contract based upon responses to this notice is solely within the discretion of the Government. The information received will normally be considered solely for the purposes of determining whether to proceed on a non-competitive basis or to conduct a competitive procurement. All responses must be received by the closing date and time of this announcement and must reference the solicitation number. Responses may be submitted electronically to Megan Ault, Contract Specialist, at megan.ault@nih.gov. US Mail and Fax responses will not be accepted.
- Web Link
-
FBO.gov Permalink
(https://www.fbo.gov/spg/HHS/NIH/NIDA-2/HHS-NIH-NIDA-SSSA-NOI-14-637/listing.html)
- Place of Performance
- Address: National Institute of Mental Health, BG 49 RM 5A60, 49 Convent Drive, Bethesda, Maryland, 20814, United States
- Zip Code: 20814
- Zip Code: 20814
- Record
- SN03477334-W 20140824/140822235547-65b8b2c3c7c2a1dab8e78e5a6d2b7d0b (fbodaily.com)
- Source
-
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