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Merge pull request #61 from ZhuangLab/master
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Update license from Zhuang lab
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emanuega authored Apr 20, 2020
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4 changes: 4 additions & 0 deletions README.md
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[![CircleCI](https://circleci.com/gh/emanuega/MERlin/tree/master.svg?style=svg)](https://circleci.com/gh/emanuega/MERlin/tree/master)
[![codecov](https://codecov.io/gh/emanuega/MERlin/branch/master/graph/badge.svg)](https://codecov.io/gh/emanuega/MERlin)
[![DOI](https://zenodo.org/badge/202668055.svg)](https://zenodo.org/badge/latestdoi/202668055)

# MERlin - Extensible pipeline for scalable data analysis

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execute workflows on a single computer, on a high performance cluster, or on the cloud
(AWS and Google Cloud).

If MERlin is useful for your research, consider citing:
Emanuel, G., Eichhorn, S. W., Zhuang, X. 2020, MERlin - scalable and extensible MERFISH analysis software, v0.1.6, Zenodo, doi:10.5281/zenodo.3758540

Please find the most recent version of MERlin [here](https://github.com/emanuega/merlin).

## MERFISH data analysis
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150 changes: 21 additions & 129 deletions license.md
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**Academic and/or Non-Commercial Research Use Software License and Terms of
Use**

This Agreement concerns MERLIN (the “Software”), useful for analysis of images
obtained using MERFISH. The Software was developed by George Emanuel, Stephen
Eichhorn, and Xiaowei Zhuang at Harvard University.

Using the Software indicates your agreement to be bound by the terms of this
Software Use Agreement (“Agreement”). Absent your agreement to the terms below,
you (the “End User”) have no rights to hold or use the Software whatsoever.

President and Fellows of Harvard College (“Harvard”) agrees to grant hereunder
the limited non-exclusive license to End User for the use of the Software in the
performance of End User’s internal, non-commercial research and/or academic use
at End User’s institution or company (“Institution”) on the following terms and
conditions:

1. **NO REDISTRIBUTION.** The Software remains the property of Harvard, and
except as set forth in Section 4, End User shall not publish, distribute, or
otherwise transfer or make available the Software to any other party.

2. **NO COMMERCIAL USE.** End User shall not use the Software for commercial
purposes and any such use of the Software is expressly prohibited. This
prohibition includes, but is not limited to, use of the Software in
fee-for-service arrangements or to provide research services to (or in
collaboration with) third parties for a fee. This prohibition does not
extend to use for internal research purposes within a for-profit entity. If
End User wishes to use the Software for commercial purposes prohibited
herein, or for any other restricted purpose, End User must execute a
separate license agreement with Harvard.

> *Requests for use of the Software for or on behalf of for-profit entities or
> for any commercial purposes, please contact*:
>
> Office of Technology Development
Harvard University
Smith Campus Center, Suite 727E
1350 Massachusetts Avenue
Cambridge, MA 02138 USA
Telephone: (617) 495-3067
E-mail: otd\@harvard.edu

3. **OWNERSHIP AND COPYRIGHT NOTICE.** Harvard owns all intellectual property
in the Software. End User shall gain no ownership to the Software. End User
shall not remove or delete and shall retain in the Software, in any
modifications to Software and in any Derivative Works, the copyright,
trademark, or other notices pertaining to Software as provided with the
Software.

4. **DERIVATIVE WORKS.** End User may create and use Derivative Works, as such
term is defined under U.S. copyright laws, provided that any such Derivative
Works shall be restricted to non-commercial, internal research and/or
academic use at End User’s Institution. End User may distribute Derivative
Works to other institutions solely for the performance of non-commercial,
internal research and/or academic use on terms substantially similar to this
License and Terms of Use.

5. **FEEDBACK.** In order to improve the Software, comments from End Users may
be useful. End User agrees to provide Harvard with feedback on the End
User’s use of the Software (e.g., any bugs in the Software, the user
experience, etc.). Harvard is permitted to use such information provided by
End User in making changes and improvements to the Software without
compensation or an accounting to End User.

6. **NON ASSERT.** End User acknowledges that Harvard may develop modifications
to the Software that may be based on the feedback provided by End User under
Section 5 above. Harvard shall not be restricted in any way by End User
regarding the use of such information. End User acknowledges the right of
Harvard to prepare, publish, display, reproduce, transmit and or use
modifications to the Software that may be substantially similar or
functionally equivalent to End User’s modifications and/or improvements if
any. In the event that End User obtains patent protection for any
modification or improvement to Software, End User agrees not to allege or
enjoin infringement of End User’s patent against Harvard or any of its
researchers, medical or research staff, officers, directors and employees.

7. **PUBLICATION & ATTRIBUTION.** End User has the right to publish, present,
or share results from the use of the Software.  In accordance with customary
academic practice, End User will acknowledge Xiaowei Zhuang Laboratory at
Harvard as the provider of the Software.

8. **NO WARRANTIES.** THE SOFTWARE IS PROVIDED "AS IS." TO THE FULLEST EXTENT
PERMITTED BY LAW, HARVARD HEREBY DISCLAIMS ALL WARRANTIES OF ANY KIND
(EXPRESS, IMPLIED OR OTHERWISE) REGARDING THE SOFTWARE, INCLUDING BUT NOT
LIMITED TO ANY IMPLIED WARRANTIES OF MERCHANTABILITY, FITNESS FOR A
PARTICULAR PURPOSE, OWNERSHIP, AND NON-INFRINGEMENT. HARVARD MAKES NO
WARRANTY ABOUT THE ACCURACY, RELIABILITY, COMPLETENESS, TIMELINESS,
SUFFICIENCY OR QUALITY OF THE SOFTWARE. HARVARD DOES NOT WARRANT THAT THE
SOFTWARE WILL OPERATE WITHOUT ERROR OR INTERRUPTION.

9. **Limitations of Liability and Remedies**. USE OF THE SOFTWARE IS AT END
USER’S OWN RISK. IF END USER IS DISSATISFIED WITH THE SOFTWARE, ITS
EXCLUSIVE REMEDY IS TO STOP USING IT. IN NO EVENT SHALL HARVARD BE LIABLE TO
END USER OR ITS INSTITUTION, IN CONTRACT, TORT OR OTHERWISE, FOR ANY DIRECT,
INDIRECT, SPECIAL, INCIDENTAL, CONSEQUENTIAL, PUNITIVE OR OTHER DAMAGES OF
ANY KIND WHATSOEVER ARISING OUT OF OR IN CONNECTION WITH THE SOFTWARE, EVEN
IF HARVARD IS NEGLIGENT OR OTHERWISE AT FAULT, AND REGARDLESS OF WHETHER
HARVARD IS ADVISED OF THE POSSIBILITY OF SUCH DAMAGES.

10. **INDEMNIFICATION.** To the extent permitted by law, End User shall
indemnify, defend and hold harmless Harvard and its current or future
directors, trustees, officers, faculty, medical and professional staff,
employees, students and agents and their respective successors, heirs and
assigns (the "Indemnitees"), against any liability, damage, loss or expense
(including reasonable attorney's fees and expenses of litigation) incurred
by or imposed upon the Indemnitees or any one of them in connection with any
claims, suits, actions, demands or judgments arising from End User’s breach
of this Agreement or its Institution’s use of the Software except to the
extent caused by the gross negligence or willful misconduct of Harvard. This
indemnification provision shall survive expiration or termination of this
Agreement.

11. **GOVERNING LAW.** This Agreement shall be construed and governed by the
laws of the Commonwealth of Massachusetts regardless of otherwise applicable
choice of law standards.

12. **NON-USE OF NAME.** Nothing in this License and Terms of Use shall be
construed as granting End Users or their Institutions any rights or licenses
to use any trademarks, service marks or logos associated with the Software.
You may not use the terms “Harvard” (or a substantially similar term) in any
way that is inconsistent with the permitted uses described herein. You agree
not to use any name or emblem of Harvard or any of its subdivisions for any
purpose, or to falsely suggest any relationship between End User (or its
Institution) and Harvard, or in any manner that would infringe or violate
any of Harvard’s rights.

13. End User represents and warrants that it has the legal authority to enter
into this License and Terms of Use on behalf of itself and its Institution.

The MIT License

Copyright (c) 2019 Harvard University

Permission is hereby granted, free of charge, to any person obtaining a copy
of this software and associated documentation files (the "Software"), to deal
in the Software without restriction, including without limitation the rights
to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
copies of the Software, and to permit persons to whom the Software is
furnished to do so, subject to the following conditions:

The above copyright notice and this permission notice shall be included in all
copies or substantial portions of the Software.

THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
SOFTWARE.

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