Resources

Empowering Discovery

This page is a collection of resources to help the research community better understand ClearLight Biotechnologies' history, technology, services, and path forward. Also, please visit our Frequently Asked Questions (FAQs). If you don’t see what you are looking for, please contact us.

Our mission is to revolutionize the diagnostic, prognostic, and predictive treatment of disease by enabling next generation technologies for non-destructive processing and digitally analyzing tissue in 3D. We are developing an automated instrumentation platform based on the CLARITY lipid-clearing technique.

 

Empowering Researchers

California Pharmaceutical and Biotechnology companies have more than 1,300 potential therapies in the pipeline that have the potential to help people facing cancer, infectious diseases, rare and genetic diseases and other disease states. Countless more potential drugs are in the early stages of discovery and research phase. ClearLight aims to empower researchers in the drug discovery process to see more biology so they can explore further.

Creating Cures Community

We applaud the research community and their involvement in the drug discovery and development process. These are the modern heroes who will create the cures of tomorrow for the disease(s) that impact human potential and decrease lifespan. Please join our Creating Cures community. You’ll receive our email newsletter periodically and have an opportunity to have your voice be heard as well.

ABOUT THE INNOVATORS

Meet the Inventor

Dr. Karl Deisseroth, professor of bioengineering and psychiatry at Stanford University, founded ClearLight based on the CLARITY lipid-clearing technique he and colleagues invented at Stanford University. Dr. Deisseroth has a long list of publications, honors and awards, including the 2015 Lurie Prize in Biomedical Sciences for the development of CLARITY and optogenetics. His scientific achievements have spawned additional research and inventions that have revolutionized the study of the brain and have led to major advances in neuroscience and biomedical engineering. He continues to serve ClearLight Biotechnologies as a Scientific Advisor. Follow Dr. Deisseroth on twitter at @KarlDeisseroth.

Who is ClearLight Diagnostics?

ClearLight Diagnostics was the former name for ClearLight Biotechnologies. The new name more accurately reflects the current short and longer-term business plan, as well as the future potential commercialization plan to introduce a Research Use Only (pharmaceutical and academics) platform into the market.

ABOUT THE TECHNOLOGY

CLARITY Tissue Clearing Genesis

The CLARITY method was originally developed at the Karl Deisseroth Lab at Stanford University. It was first made public in a paper published in Nature in 2013. [ K Chung, J Wallace, S-Y Kim, S Kalyanasundaram, AS Andalman, TJ Davidson, JJ Mirzabekov, KA Zalocusky, J Mattis, AK Denisin, S Pak, H Bernstein, C Ramakrishnan, L Grosenick, V Gradinaru, and K Deisseroth. Structural and molecular interrogation of intact biological systems. Nature (2013) 497: 332-337.]

ClearLight Biotechnologies was founded in 2014 by Karl Deisseroth MD, PhD, the inventor of CLARITY, Optogenetics, and STARmap technologies. It is an early stage company focused on developing automated instrumentation and associated reagents to simplify and expedite non-destructive 3D tissue analysis.. The platform will enable an end-to-end solution for 3D analysis of preclinical and clinical models of disease.

A World of Opportunity

ClearLight Biotechnologies has an exclusive, worldwide license agreement with Stanford University for development and commercialization of CLARITY for diagnostic and clinical applications. We are committed to a future where researchers and clinicians worldwide have access to automated instruments bringing the power of CLARITY to clinical applications. Imagine a new 3D platform that empowers better clinical diagnosis, prognosis, and predictive applications, and is utilized in every research and pathology laboratory around the world. If you want to collaborate in bringing this opportunity to fruition, you can talk to our scientific staff.

Making Brains Transparent

Scientists can make brains transparent, so they can be labelled with molecular markers and imaged. The technique, CLARITY, invented by ClearLight Founder & Scientific Advisor, Karl Deisseroth, MD, PhD., enables the 3D visualizations seen in this Nature video.

 

We Value Our Relationships

We're looking for early adopters who value the potential of a 3D revolution in immunohistochemistry (IHC). ClearLight’s collaborative and pilot lab services will include tissue clearing using the CLARITY method, immunostaining, 3D imaging (multiplexed fluorescence), and we are developing the capability to perform true 3D spatial analysis in 3D.  The team continues to develop our capabilities and would love to work with you to address your research needs.  Contact us to discuss your project with our team of scientists.

LEARN MORE ABOUT CLARITY

CLARITY Tissue Clearing Process

CLARITY was born from the need to overcome the opacity of lipids in brain tissue, which caused light to scatter during microscopic visualization of neurons, thereby obscuring image quality. CLARITY allows a tissue sample to be rendered optically clear, retain its three-dimensional integrity and allows for tissue staining and re-interrogation multiple times. It works for human and mouse brain tissue and most other intact human and rodent biological tissues.

Creating See-through Tissues

In the CLARITY method, a tissue sample is first embedded in a hydrogel. This hydrogel provides a three-dimensional matrix that supports the tissue sample and retains the structural integrity and spatial orientation of the critical tissue components. The non-critical elements such as lipids are removed using detergent solutions. Light can then penetrate the tissue sample rendering it “see-through” or transparent and thus permeable to molecules.

Tissue Staining

Researchers employ multiplexed IHC staining to identify cell phenotypes of interest within the tissue microenvironment. Since the sample is embedded and intact within the cleared hydrogel matrix, the stained tissue has the potential to be imaged entirely in three dimensions. The tissue’s transparency enables 3-D imaging of subcellular components such as DNA, RNA, and proteins for analysis of heterogeneous cellular interactions within the tumor microenvironment of a tissue.

CLARITY Advantage over Creating 3D Images from 2D Slices

2D thin section tissue imaging requires tissue destruction and digital reconstruction. Alternatively, the CLARITY methodology is non-destructive and allows the tissue to remain intact enabling a scientist to spatially identify the interaction of a variety of cellular phenotypes within the same tissue sample.

Passive Clearing versus Active Clearing

Passive tissue clearing with CLARITY is a straightforward and inexpensive, but a much slower process compared to active clearing. Active tissue clearing utilizes electrophoresis to apply electric fields to accelerate the removal of lipids from tissues and is more suitable technique for future clinical applications that require a shorter turnaround time.. The 3D tissue clearing technology, CRYSTAL, invented by Professor Adriano Aguzzi, M.D, Ph.D., and Daniel Kirschenbaum, M.D, Ph.D. at the University of Zurich and the University Hospital Zurich has the advantage of using a focused detergent-ion stream tailored to the sample to be optically cleared. Previous detergent electrophoretic methods for optical clearing, rely on an electric current irrespective of sample morphology.

Thus, in these approaches the ion stream traverses the sample container along the path of least electrical resistance, which is simply the surrounding buffer solution. Modifying this with the CRYSTAL technology, to a focused electrophoretic approach enhances the clearing process multi-fold and allows the clarification of a 1 mm thick tissue biopsy in 30 minutes. CRYSTAL is easy to miniaturize and parallelize, and it has been successfully utilized in the academic setting to test multiple drugs in animal models of disease.

Multiplex Immunohistochemistry (IHC) staining

IHC Staining is the general term used to describe the use of colored, often fluorescent, compounds that bind to very specific antigenic sites within a tissue sample. It is useful, because it can stain and provide visual information confirming the presence and precise location of a wide array of specific antibodies - that can only be present as a reaction to a specific antigen — thus the detection of the presence of specific antibodies through IHC staining is an important diagnostic tool.

IHC staining has been utilized as far back as the 1940s and is now routinely used in diagnostic medicine, bio-medical research, and histopathology.

In Multiplex IHC Staining, multiple sites within a single tissue sample are stained at once, with different colors representing different targets, or different cell types. This is especially helpful in the field of immuno-oncology as it allows for imaging the complex variety of cells within a tumor microenvironment.

ClearLight Biotechnologies in the News

What Others are Saying about CLARITY

Francis Collins, Director of the National Institutes of Health (NIH)

“CLARITY is powerful. It will enable researchers to study neurological diseases and disorders, focusing on diseased or damaged structures without losing a global perspective. That’s something we’ve never before been able to do in three dimensions.” Francis Collins, Director of the National Institutes of Health (NIH)

“In surgical pathology, time is of the essence. By doing away with paraffin embedding and microtome cutting, the CRYSTAL technology allows for acquiring holographic ultra-high-resolution images of specimens more quickly than with conventional histology,” Professor Aguzzi, Director of the Institute of Neuropathology.

“The CLARITY technology holds promise to revolutionize spatial analysis by enabling 3D analysis of thick (up to 1000-micron) tumor to achieve more biologically relevant information regarding tumor heterogeneity and key spatial relationships in the tumor microenvironment.” Sunil Badve, MD - Joshua Edwards Professor of Pathology and Laboratory Medicine and Director of the Translational Genomics Core.

External Resources

Spatial analysis can be performed for select biomarkers, please contact us to find out if your target of interest is one of them. Imaging is currently performed on select fields of view instead of the entire sample.

Submission Guidelines

 Terms of Service Agreement                                             

  1. General Terms

These terms and conditions (“Terms”) apply to your purchase of the tissue clearing and imaging services (the “Services”) from ClearLight Biotechnologies, LLC (“we” or “us”), described in the description of services at https://clearlightbiotechnologies.com/ submitted by you (“you”) and accepted by us. The Terms form the entire contract between you and us with respect to your purchase of the Services. If, however, you are contracting for Tru3D Spatial services, a separate contract will be required, which will apply to such services. By transmitting your signature electronically (for example, clicking “I Agree”), you agree to the Terms.

2   Shipping and Payment.   

Payment is due upon receipt of an invoice from us, pursuant to the payment terms set forth therein. We will invoice you upon completion of the Services and prior to delivering any Deliverables to you.  The submission requirements page https://clearlightbiotechnologies.com/ specifies the manner in which tissues must be packaged and shipped in order for the Services to be performed.  You will be responsible for payment and procurement of a nationally recognized carrier to deliver the tissue samples to us.  If Services cannot be performed because the tissue samples are not packaged in such proper manner and/or there is a shipping issue which prevents us from performing the Services, we will notify you.

  1. Performance of Services

We will provide the Services as an independent contractor, using methods, materials, equipment, and/or related intellectual property owned or controlled by us or our affiliates (collectively “Our Technology”) to provide you with data, video and images produced by us as a direct result of the Services, as described on https://clearlightbiotechnologies.com/ (collectively, “Deliverables”). We will make a good faith effort to provide the Services and will notify you if substantial delays are likely or if we are unable to conduct the Services on your tissue samples. We will comply with all laws and regulations generally applicable to the Services.

  1. Client Materials and Data

You will provide us with tissue samples in compliance with applicable laws and regulations, including privacy laws and regulations, as well as relevant safety information.  You will supply tissue samples in sufficient amounts, and with the other characteristics of tissue samples, that we need to perform the Services, including without limitation any certification or documentation of tissue samples we reasonably request of you. The tissue samples and information you provide us must not contain any personally identifiable information.  Our performance of the Services is contingent on your providing us with de-identified samples and your compliance with all applicable privacy laws.  Your tissue samples, and all information specifically related to your tissue samples, whether you provide it or we generate it in the performance of Services (such information collectively referred to as “Data”), shall be subject to the confidentiality provisions of Section 8. Upon completion of the Services, we will maintain all tissue samples not consumed in the Services for a period of 30 days after data is distributed to the client and thereafter will discard all such tissue samples. Samples that do not meet the sample requirements and submission guidelines will be discarded immediately. We will store all Data for a period of 30 days and thereafter the Data will be deleted from our servers and we will only store compiled client reports.

  1. Use Limitations

You agree to use Deliverables for research use only, only for lawful purposes and not for any diagnostic or therapeutic purpose. Without limiting the foregoing, you shall not directly or indirectly furnish materials or information provided hereunder to any entity, or destination, or for any use, except in full accordance with all applicable laws and regulations, including without limitation export control and trade sanctions laws and regulations of the United States.

6      Ownership, Intellectual Property; no Reverse Engineering

As between us and you, and except as provided in Section 8, whether or not copyrightable or patentable (collectively, the “Client Inventions”). Client Inventions shall not include the Services or any improvements or modifications thereof, whether developed before or during the performance of the Services. You shall not, by virtue of the Services performed hereunder, obtain any license or other rights in any of Our Technology, and you shall not (a) use Deliverables other than as set forth in Section 5, (b) independently recreate the Deliverables or any materials that are proprietary to us, (c) sell or otherwise use the Deliverables for commercial purposes whether or not commercialized for research use or (d) file any patent application containing a claim to any subject matter derived from the Services, without our prior written consent.  You agree that you will not decompile, disassemble or reverse engineer all or any part of our technology used in the Services. In the event that such activity is expressly permitted by applicable law notwithstanding this limitation, you shall provide us with written notice prior to such reverse engineering activity, information regarding the intended method of reverse engineering, its purpose and the legal authority for such activity and shall afford us a reasonable period of time before initiating such activity in order for us to evaluate the activity and/or challenge the reverse engineering activity with the appropriate legal authorities. You shall refrain from such reverse engineering activity until such time as any legal challenge is resolved in your favor. Reverse engineering includes, without limitation, attempting to (a) derive the source code (b) modify, translate, reverse engineer, decompile, disassemble or otherwise attempt (i) to defeat, avoid, bypass, remove, deactivate or otherwise circumvent any software protection mechanisms, including without limitation any such mechanism used to restrict or control the functionality of the data; (c) alter, adapt, modify or translate data in any way for any purpose, including without limitation error correction; or (d) thereafter, reverse engineer or otherwise attempt to discern the trade secret information of the Services.  In addition to any other rights and remedies that we may have under the circumstances, you shall be required in all cases to pay royalties to us, in an amount consistent with industry standards.

7      Non-Exclusivity

Unless expressly agreed in writing, that are identical or similar to Deliverables, provided that in doing so, we will not use any information received from you to perform Services for any third party.

 8      Confidentiality

We will treat all tissue samples and Data provided by you as proprietary and confidential to you, and will not disclose such confidential information to any person except to our employees, and subcontractors as necessary for purposes of providing the Services, and then only subject to a written confidentiality agreement that includes the requirements specified herein. If we disclose any information or materials comprising Services to you, you will treat such information and materials as proprietary and confidential to us. Each party shall protect the proprietary and confidential information or materials of the other party by using the same degree of care as such party uses to protect its own materials and information, but in any event no less than a reasonable degree of care. Notwithstanding any other provisions herein, however, each recipient party shall have no obligation to the other party for any information or material that is (a) already known to the recipient party; (b) publicly known other than by a wrongful act of the recipient party; (c) received from a third party lawfully entitled to disclose it; (d) disclosed pursuant to an enforceable order of a court or administrative agency; and/or (e) independently developed by or for the recipient party. We will own our laboratory notebooks or other records maintained with respect to the Services; but to the extent such notebooks or records contain any raw data or other confidential information of yours, such data and confidential information will continue to be your property, and the parts of the notebooks and records that contain your confidential information will be subject to our obligations of nonuse and confidentiality; provided however, that we may use the tissue samples and raw data provided by you and the Services provided to you, as part of our ongoing research to improve the provision of the Services to you and to third parties. You and we shall ensure, both during and after the performance of the Services, that (i) persons who are not bound by a confidentiality agreement consistent with the Terms shall not have access to the Services and (ii) persons who are so bound are put on written notice that the Services contain trade secrets, owned by and proprietary to us.

9      Warranty

9.1     Our Limited Warranty

Our sole warranty for the performance of Services is that the Services will be performed using due care in accordance with (a) the Terms and (b) laws, regulations and generally prevailing industry standards applicable to such Services. We are warranting that if the tissue samples are submitted as per our website guidelines, the Deliverables will contain the results described in the website guidelines.

9.2     Remedies

For valid warranty claims made, we will refund to you the fees actually paid for the particular Services giving rise to the breach of warranty.

9.3     Limitations

THE WARRANTY SET FORTH IN THIS SECTION 9 IS IN LIEU OF ANY AND ALL OTHER WARRANTIES RELATING TO THE SERVICES, EXPRESS OR IMPLIED, INCLUDING, WITHOUT LIMITATION, ANY IMPLIED WARRANTIES OF SATISFACTORY QUALITY, MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE, OR THAT DELIVERABLES OR USE THEREOF WILL NOT INFRINGE ANY THIRD PARTY INTELLECTUAL PROPERTY RIGHT. WE SHALL NOT BE LIABLE UNDER ANY LEGAL THEORY, FOR ANY INDIRECT, SPECIAL, OR CONSEQUENTIAL DAMAGES OR FOR LOSS OF PROFITS OR LOSS OF BUSINESS, EVEN IF WE HAD NOTICE OF THE POSSIBILITY THEREOF. OUR LIABILITY TO YOU FOR BREACH OF ANY PROVISION OF THESE TERMS (OTHER THAN BREACH OF (A) THE CONFIDENTIALITY PROVISIONS OF SECTION 8 OR (B) THE WARRANTY IN THIS SECTION 9 FOR WHICH LIABILITY IS LIMITED TO REFUND AS SPECIFIED HEREIN) SHALL BE LIMITED TO DAMAGES IN AN AMOUNT NOT TO EXCEED THE FEE TO BE PAID FOR THE SERVICES TO WHICH THE BREACH RELATES.

10 Indemnification

Except to the extent caused by our gross negligence or willful misconduct, you shall indemnify and hold harmless us and our affiliates and our and their respective officers, directors, employees and agents (“Indemnified Party”) from and against any and all expenses (including, but not limited to, reasonable attorney’s fees) and losses incurred by any such Indemnified Party in connection with any claim asserted by a third party arising out of or based on (a) the Services or your use of the results of the Services; and/or (b) any product or service of yours that is based in whole or part on the Deliverables, or any portion or derivative thereof; and/or the Agreement.

11 Communication, Changes, Termination

11.1 Communication

You must designate a single person (“Customer Contact”) to act as your authorized representative. Such person shall have complete authority to transmit instructions, receive information and data, and to request changes to the Services. To facilitate the Services, we may communicate with and act on instructions provided by other persons within your organization, however we will not accept any liability for a failure to communicate with, or act on instructions provided by, a person other than your Customer Contact.

11.2 Changes

Changes to the Services must be agreed by both parties in writing and may require changes in the fees or timelines.

11.3 Termination

We may terminate the Agreement if (a) you breach any material provision of the Terms and fail to remedy the breach to our satisfaction within 30 days after our written notice to you; or (b) we determine that biosecurity, biosafety, and/or feasibility reasons prevent or are likely to prevent the performance of the Services. Termination of Services in progress will result in a partial charge commensurate with the percentage of Services completed at the time of cancellation.

12 Assignment

The Agreement may not be assigned by either party without the consent of the other party, except that each party may assign the Agreement to an affiliate or to any other party to whom it transfers the business and assets related to the Agreement, provided that such assignee assumes all the rights and obligations of its assignor.

  1. Governing Law.

Delaware state law governs this Agreement without regard to its conflict of law’s provisions.

  1. Disputes.

ANY DISPUTE OR CLAIM RELATING IN ANY WAY TO THE SERVICES OR THE TERMS WILL BE RESOLVED BY BINDING ARBITRATION, RATHER THAN IN COURT, except that you may assert claims in small claims court if your claims qualify. The Federal Arbitration Act governs the interpretation and enforcement of this provision; the arbitrator shall apply Delaware law to all other matters. Notwithstanding anything to the contrary, any party to the arbitration may at any time seek injunctions or other forms of equitable relief from any court of competent jurisdiction. WE EACH AGREE THAT ANY AND ALL DISPUTES MUST BE BROUGHT IN THE PARTIES’ INDIVIDUAL CAPACITY AND NOT AS A PLAINTIFF OR CLASS MEMBER IN ANY PURPORTED CLASS OR REPRESENTATIVE PROCEEDING. BY ENTERING INTO THIS AGREEMENT AND AGREEING TO ARBITRATION, YOU AGREE THAT YOU AND WE ARE EACH WAIVING THE RIGHT TO FILE A LAWSUIT AND THE RIGHT TO A TRIAL BY JURY. IN ADDITION, YOU AGREE TO WAIVE THE RIGHT TO PARTICIPATE IN A CLASS ACTION OR LITIGATE ON A CLASS-WIDE BASIS. YOU AGREE THAT YOU HAVE EXPRESSLY AND KNOWINGLY WAIVED THESE RIGHTS.

  1. Changes.

We reserve the right to modify the Agreement, in our sole discretion, at any time, to apply to Services subsequently ordered by you. Such modifications may be posted through the Terms, on our website for the Services or when we notify you by other means. We may also change or discontinue the Services, in whole or in part. It is important that you review the Agreement whenever we modify it because your continued use of the Services indicates your agreement to the modifications.

  1. Termination.

We may, in our sole discretion and without notice, restrict, deny, terminate the Agreement or suspend the Services, effective immediately, in whole or in part, if we determine that your use of the Services violates the Agreement, is improper or substantially exceeds or differs from normal use by other users, raises suspicion of fraud, misuse, security concern, illegal activity or unauthorized access issues, to protect the integrity or availability of the Services.

  1. Miscellaneous Provisions.

Nothing in the Agreement, the Terms, or the Services shall be construed to create a partnership, joint venture or employment relationship between us.  If any provision of the Agreement shall be determined to be invalid or unenforceable, such determination shall not affect the validity of the other provisions of the Agreement. Waiver by either party or the failure by either party to claim a breach of any provision of the Agreement shall not be deemed to constitute a waiver or estoppel with respect to any subsequent breach of any provision of the Agreement. If you are entering into the Agreement on behalf of a company or other legal entity, you represent that you have the authority to bind such entity and its affiliates to these terms and conditions as its authorized representative, in which case the terms “you” or “your” will refer to such entity and its affiliates as well as you. If the legal entity that you represent does not agree with these terms and conditions, you must not accept this Agreement or use or access the Services as an authorized representative.

Tissue Sample Requirements: