70-U6900-26-CP319_072826 SVI Upgrade Existing Huygens licenses &Huygens Everywhere license Sole Source $65,494.pdf.PDF

UNM Proposed Sole Source Form – Rev 04/07/2021

Proposed Sole Source Purchase Form Pursuant to N ew M exico Procurem ent law , the UN M Purchasing D epartm ent w ill post your com pleted form on the UN M

Sunshine Portal and the State of N ew M exico Procurem ent w ebsite for 30 days prior to purchase of the goods/services.

I. GENERAL INFORMATION. PLEASE PROVIDE THE FOLLOWING:

Date of Request 07/10/26 Requisition Number (If Applicable) Request Submitted by: Michael Paffett Title Research Facility

Director Department UNMCCC ALMSR Shared Resources Email mpaffett@salud.unm.edu Phone 2-1437

Proposed Vendor Scientific Volume Imaging b.v. Amount $65,494.00 Vendor Address Marathon 9E

1213 PE Hilversum, The Netherlands

Term of Purchase

One time-purchase

Buyer Team - See Commodity list at http://purchase.unm.edu/department-information/comm-code-listing.pdf

Provide a basic description of goods/services to be provided:

This sole source is for a 1-year Maintenance and Upgrade (M&U) software licenses to upgrade all of our existing Huygens and Localizer licenses to the most recent versions AND receive any new update for the following year and for a Huygens Everywhere license that can support 3 concurrent users simultaneously on 3 different workstations.

Huygens offers seamless solutions for Deconvolution, Image Restoration (Chromatic Aberration, Cross Talk, Stitching, Bleaching, and Hot&Cold Pixel and Drift/unwanted movement corrections), Visualization and Analysis (Object Analysis & Quantification, Tracking, Colocalization analysis, and Cluster analysis,) of 2D, 3D and multi-channel and times series image data that are critical tools for the UNMCCC ALMSR.

Why is this purchase needed?

Purchasing software maintenance and upgrade software maintenance agreements for ALL our existing Huygens and Localizer licenses is a critical to ensure that the HSC and UNMCCC imaging community have the latest tools and technology to conduct world class biomedical research.

Purchasing an additional Huygens Everywhere License is needed for a recently funded project where we are expanding the computational and image analysis infrastructure of the Advanced Light Microscopy Shared Resource to support more users performing image quality control and analysis in our facility.

II. BASIS FOR SOLE SOURCE PROCUREMENT. CHOOSE APPLICABLE BOX(ES) AND

PROVIDE ADDITIONAL INFORMATION, AS REQUESTED:

☒ Proprietary item, technology or service only available from the proposed vendor. (Check box and describe proprietary component)

Considering this sole source is to upgrade all our existing Huygens and Localizer licenses, the upgrade is only available from the developer, Scientific Volume Imaging.

☒ Compatibility requirement with existing item, technology or service. (Check box and describe compatibility requirement)

Yes, these are license upgrades are for our existing software licenses.

Yes, this additional Huygens Everywhere license is an expansion of our existing Huygens software license.

☒ Renewal of support/maintenance/subscription of software, technology or other intellectual property. (Check box and describe)

The software update is a 1-year M&U that will update all of our existing licenses from all prior license versions that are 6-7 years old. Many features have been improved in the latest software versions and numerous new features that will help our imaging community better understand their research imaging science. We will also receive any new updates 1-year from purchase of this M&U.

The software addition will come standard any new version or feature releases for a period of 1-yr post purchase.

☐ Other Basis for Sole Source: Please describe below:

III. SUPPLEMENTAL DETAILS. PLEASE PROVIDE ADDITIONAL INFORMATION AS

REQUESTED BELOW:

Describe in detail the unique capabilities of the proposed vendor’s goods/service and/or personnel performing the work and why this constitutes the only source. Focus on what is unique about the goods/service and why no other vendor could meet your needs.

Unique features of HUYGENS:

Features Included in AIVIA Apex (CellBio and Neuro):

1. HUYGENS offers seamless solutions for Deconvolution, Image Restoration (Chromatic Aberration, Cross Talk, Stitching, Bleaching, and Hot&Cold Pixel and Drift/unwanted movement corrections), Visualization and Analysis (Object Analysis & Quantification, Tracking, Colocalization analysis, and Cluster analysis,) of 2D, 3D and multi-channel and times series image data. Huygens works for all types of light-microscopic data. Depending on your needs you can choose between Huygens Essential, Professional or Core. For analyzing single molecule localization microscopy

(SMLM) data, we have developed Huygens Localizer. With the introduction of the Huygens Quality Control option in 2024, which detects and corrects imaging issues, and the ability to save image processing workflows, Huygens underscores the importance of image quality and reproducibility for obtaining reliable scientific results, as is also recognized by the scientific community (https://quarep.org/).

HARDWARE ENVIRONMENT

2. The HUYGENS software is very scalable from laptops to computer clouds (with numerous systems connected), large servers, and computer nodes. So, Huygens is excellently geared to facilitate single and many users, and large groups via single IT management.

3. In default mode, HUYGENS uses CPU and GPU power for specific configurations. More high-end options are available for increasing performance regarding the number of CPUs and GPUs, and the type of GPU cards (Nvidia). Huygens is perfectly suitable for simultaneous usage of multiple super-fast GPU cards and up to 256 hyper-threaded CPU cores. Use of extra RAM is unlimited and involves no extra charges.

4. You can use Huygens as a node-locked license on a dedicated machine (off-line and on-line) or Everywhere floating via a secure login for multiple users sharing one Huygens account (multiple seats). Ideal for single users, and for Imaging Facilities who offer their expertise, software and equipment to many labs. Furthermore, from every seat or license remote display works as well (secure fixed connections to specific IP addresses) So very many users can work directly on their own computers with Huygens making the investment much more effective.

5. Huygens is perfectly suited for high-throughput and high-content image processing with the Workflow Processor and Huygens Core. The Workflow Processor in can process many images with pre-made processing pipelines. Huygens Core be called from any node/job management software (pipeline environment) using the Command Line Interface (CLI), or used in combination with Huygens Remote Manager (HRM). This HRM is an open source task manager that acts as a webinterface to Huygens Core. It can be used with any web-browser, and is therefore ideally suited for scheduling many image processing jobs and serving many different users from any location. The user-friendly HRM interface accepts templates from Huygens Essential and Professional, and facilitates an optimized connection to OMERO (open source) image data servers for data import and export.

6. HUYGENS can run on all current and recent Windows, Mac, and Linux systems. While under maintenance people can migrate to another platform if that suits their needs better.

7. HUYGENS is known for being extremely stable in its performance. In the past 28 years, we have been confronted with only a few rare cases where the Huygens software closed unexpectedly. In these instances, we provided immediate fixes (within 24 hours). We have a track record of releasing two major upgraded Huygens versions per year and regular updates (1-2 times per two weeks). With our Spring and Fall release many improvements, and new features and options are included. Our excellent support has been highly rated by many Huygens users from all over the world.

SPECIFICALLY FOR WIDEFIELD, CF 1Ph&2Ph, SPINNING DISC, SORA, STED, AIRYSCAN, LIGHTSHEET:

8. HUYGENS is the Golden Standard in deconvolution world-wide. It has the best possible deconvolution algorithms currently available [1]. These Maximum Likelihood Estimation based algorithm are fully validated and have been used in many high-ranking publications [2]. We have implemented fast versions of the MLE algorithm (GMLE and CMLE), which work extremely fast and offers very high quality results. Algorithms in other packages that include a filtering-based algorithm are extremely prone to artifacts, such as noise enhancement and signal removal around high intensity objects (so-called ringing effects).

9. Choose the Batch Feeder for automatic, instant deconvolution during acquisition. User only needs to select the ‘getting from’ and ‘going to’ folders. Excellent image quality to start the analysis with. Works on all microscopy types and brands.

10. Or select the intuitive Workflow Processor to include all or several steps in your image analysis workflow: deconvolution, image restoration, visualization and analysis for massive amounts of datasets via templates made by clicking a single button by the user. Simply drag and drop the tasks, pick the templates and get them done.

11. HUYGENS outperforms the resolution improvement that you may obtain with other software. We typically improve the resolution 1.5-4 times and signal 8 times [3], but this can be higher even. For example, Huygens can resolve structures that are 90 nm spaced on nanorulers (GATTAquant) which have been imaged with a Zeiss Airyscan (standard mode). This 90 nm resolution is unprecendented. Similarly, Huygens offers the best possible resolution and signal gain that can be obtained from STED images. Excellent deconvolution and image restoration are key for all further analysis.

12. HUYGENS works with ultra-fast ray-tracing for its visualization. We offer insights into your datasets. The big advantage is that it works on all hardware and needs no specific graphical card. No other manufacturer uses that technique as it requires a lot of extra programming to get it working properly. Most manufacturers purchased the polygon software library from Amira which smoothens the images thus hiding essential details. A second major drawback of polygon-based techniques is that it requires specific and expensive graphical cards, whereas Huygens visualization can be used on any computer.

13. HUYGENS uses by default PSF based on unique specific PSF generators are equipped to accurately model PSFs for nearly all types of optical systems ranging from widefield, confocal and Light Sheet towards super-resolution techniques such as 2D-3D (Matrix) STED, Array (Airyscan) Detector and single molecule localization microscopy (SMLM). Huygens is the sole software package that includes PSF aberrations due to imperfections in the light sheet and irregularities in sample structure. With offering solutions for all types of microscope modalities, we have proven to be a company that operates at the forefront of microscopy developments. For example, we were the first with a PSF model for STED and STED 3D deconvolution.

14. Huygens allows users to distill experimental PSFs from images of sub-resolution structures (such as beads). The use of an experimental PSF ensures that optical aberrations of the specific microscope that is being used are included in the restoration process.

15. HUYGENS is the only image processing company that offers a full range of restoration tools that can both estimate and correct for specific imaging pitfalls (like for example crosstalk, bleaching, stabilization issues, and chromatic aberration). With additional stitching and fusion tools for multiview light sheet data, and all the visualization and analysis options (3D object analysis, colocalization analysis, object tracking), Huygens offers complete workflows for many imaging questions.

16. HUYGENS unique Image Quality Control option is the only QC tool that can accept nearly any type of microscopy image which it meticulously screens for imaging artifacts. Many of the detected issues can be fixed instantly with the available restoration options in Huygens. With this option, and the possibility to saving processing templates and workflowss, we address concerns in the imaging community (https://quarep.org/) about preserving access to quantitative and reproducible light microcopy image data [4].

17. Huygens offers Object Analysis to get both visual and quantitative information via easy to use presets to run a full analysis of your 3D/multi-channel/time series with a single mouse-click to measure, count cells or any smaller objects inside instantly. Make ROI’s, Anchors, cross channel references etc. Excellent Object Analysis Workflow designer that integrates easily with the overall Workflow Processor. Exporting data and images to all default spreadsheets and MatLab.

18. Find 11 Colocalization coefficients in the HUYGENS Coloc Option, each can be presented in a unique 3D surface map to visualize the resulting object colocalization as well. Offers Region of Interest to tailor on the most interesting part of the dataset.

19. In the HUYGENS Object Tracker you can track the movement of particles and cells over time. Includes AI algorithms which will be automatically trained to detect and track new objects. It includes a unique track analyzer with many features. Via templates previous learning experiences can be re-used and exported (MatLab & all main spreadsheet programs).

20. The HUYGENS Stitcher works for all microscopy types to fit tiles in both 2D and 3D together. Offers unique 3D precision stitching also with 0% overlap. Also unique is the automatic, intelligent vignetting correction as part of the excellent wizard.

SPECIFICALLY for SMLM:

21. HUYGENS Localizer offers a unique quantifiable solution to image, analyze and quantify all types of Single Molecule Light Microscopic images (e.g. PALM, STORM, DNA-paint) with object analysis, cluster analysis and both visual and quantitative output [5].

22. Our scientific staff has performed in collaboration research groups quantification studies which prove that Huygens deconvolution offers reliable and quantifiable results [6,7,8].

23. Last but not least, our support team is famous for their excellent support. We advise users on how to acquire images properly, process them with Huygens and obtain reliable results from the images. For customer testimonials, see https://svi.nl/SviCustomerTestimonials

References

1. Microscope Image Processing”, Q. Wu, F. A. Merchant, K. R. Castleman, Academic Press, Elsevier, 2008 p.p. 339-355

2. For only a selection of references, we like to refer you to: https://svi.nl/HuygensReferences .

3. Vincent Schoonderwoert, Remko Dijkstra, Grazvydas Luckinavicius, Oliver Kobler, Hans van der Voort, Huygens STED Deconvolution Increases Signal-to-Noise and Image Resolution towards 22 nm, Microscopy Today, Volume 21, Issue 6, 1 November 2013, Pages 38–44, https://doi.org/10.1017/S1551929513001089 Note: The improvement in resolution and signal that can be obtained, relies on the quality of the raw data and the microscopy type that has been used. In our 30 years of existence, we not yet been confronted with images from other software that show an equal or higher quality than what can be obtained with the Huygens Software.

4. Robin A Pelle, Michel Ram, Peter Hemmerich, Amy L Bottomley, Louise Cole, Rolando Berlinguer- Palmini, Hans T M van der Voort, Nicolaas T M van der Voort, Vincent T G Schoonderwoert, The Impact of Image Quality on Reliable and Specific Colocalization Analysis, Microscopy Today, Volume 32, Issue 6, November 2024, Pages 20–29, https://doi.org/10.1093/mictod/qaae091

5. Peter J Verveer, Daniel Sevilla-Sanchez, Paul C Bloembergen, Nancy Adam, Vincent TG Schoonderwoert, Hans TM van der Voort, Fast Analysis of 2D and 3D Single-Molecule Localization Microscopy Data with Huygens Localizer, Microscopy Today, Volume 28, Issue 2, 1 March 2020, Pages 20–

25, https://doi.org/10.1017/S1551929520000024

6. Lee JS, Wee TL, Brown CM. Calibration of wide-field deconvolution microscopy for quantitative fluorescence imaging. J Biomol Tech. 2014 Apr;25(1):31-40. doi: 10.7171/jbt.14-2501-002.

7. Jonkman, J., Brown, C.M., Wright, G.D. et al. Tutorial: guidance for quantitative confocal microscopy.

Nat Protoc 15, 1585–1611 (2020). https://doi.org/10.1038/s41596-020-0313-9

8. for more information and references, see https://svi.nl/IntensityPreservation. Upon request, we can send more information concerning quantification studies.

9. Some of the feedback we received from customers, we have presented here:

https://svi.nl/SviCustomerTestimonials

Describe the due diligence made to locate other possible sources including communications with other universities, communications with similar providers, web searches, yellow page searches, review of advertisements and trade publications, etc.

Scientific Volume Imaging is the only source and developer of Huygens software

List the other vendors who were contacted. Please describe the specs/qualifications/criteria that the other vendors were unable to satisfy.

No other venders were contacted as there is no other source to upgrade our existing licenses.