SOURCES SOUGHT
66 -- Upgrade of Neurolucida Microscope Imaging Software
- Notice Date
- 7/25/2014
- Notice Type
- Sources Sought
- 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-SBSS-14-441
- Archive Date
- 8/16/2014
- Point of Contact
- Megan Ault,
- E-Mail Address
-
megan.ault@nih.gov
(megan.ault@nih.gov)
- Small Business Set-Aside
- N/A
- Description
- Contracting Office Address: Department of Health and Human Services, National Institutes of Health, National Institutes on Drug Abuse, Station Support Simplified Acquisitions. Introduction: This is a Small Business Sources Sought notice. This is NOT a solicitation for proposals, proposal abstracts, or quotations. The purpose of this notice is to obtain information regarding: (1) the availability and capability of qualified small business sources; (2) whether they are small businesses; HUBZone small businesses; service-disabled, veteran-owned small businesses; 8(a) small businesses; veteran-owned small businesses; woman-owned small businesses; or small disadvantaged businesses; and (3) their size classification relative to the North American Industry Classification System (NAICS) code for the proposed acquisition. Your responses to the information requested will assist the Government in determining the appropriate acquisition method, including whether a set-aside is possible. An organization that is not considered a small business under the applicable NAICS code should not submit a response to this notice. Purpose and Objectives: The purpose of this potential requirement is to upgrade 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. Product Equivalent Requirements: 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. Anticipated Period of Performance: It is expected that delivery date is approximately three (3) months after receipt of order. Capability statement /information sought: Interested organizations must provide clear and convincing documentation of their capability of providing the item(s) specified in this notice. Interested organizations that believe they possess the ability to provide the required must submit specific documentation of their ability to meet each of the project requirements to the Contract Specialist. Interested organizations must provide their Company Name, DUNS number, Physical Address, and Point of Contact Information. Interested organizations are required to identify their type of business, applicable North American Industry Classification System Code, and size standards in accordance with the Small Business Administration. The Government requests that no proprietary or confidential business data be submitted in a response to this notice. However, responses that indicate the information therein is proprietary will be properly safeguarded for Government use only. Capability statements must include the name and telephone number of a point of contact having authority and knowledge to discuss responses with Government representatives. Capability statements in response to this market survey that do not provide sufficient information for evaluation will be considered non-responsive. When submitting this information, please reference the Sources Sought notice number. All responses to this notice must be submitted electronically to the Contract Specialist and Contracting Officer. Facsimile responses are NOT accepted. All capability statements sent in response to this Sources Sought Notice must be submitted electronically (via email) to Megan Ault, Contract Specialist, at megan.ault@nih.gov in MS Word format by or before the closing date of this announcement. All responses must be received by the specified due date and time in order to be considered. The response must be received on or before July 24, 2014 by 11:00 AM (EDT). Note: This notice does not obligate the Government to award a contract or otherwise pay for the information provided in response. The Government reserves the right to use information provided by respondents for any purpose deemed necessary and legally appropriate. Any organization responding to this notice should ensure that its response is complete and sufficiently detailed to allow the Government to determine the organization's qualifications to perform the work. Respondents are advised that the Government is under no obligation to acknowledge receipt of the information received or provide feedback to respondents with respect to any information submitted. After a review of the responses received, a presolicitation synopsis and solicitation may be published in Federal Business Opportunities. However, responses to this notice will not be considered adequate responses to a solicitation. The solicitation release date is pending. The Government intends to negotiate a fixed-price purchase order. No proprietary, classified, confidential, or sensitive information should be included in your response. The Government reserves the right to use any non-proprietary technical information in any resultant solicitation(s).
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