updated readme with new license, and fixed download scripts

README.md

@@ -131,28 +131,32 @@ which will output predictions into `results/3d/mydata/test` and `results/3d/myda
 ## Citation
 If you find this code useful in your research, please consider citing our pre-publication manuscript:
 ```
-@article {Ounkomol289504,
-author = {Ounkomol, Chawin and Seshamani, Sharmishtaa and Maleckar, Mary M and Collman, Forrest and Johnson, Gregory},
-title = {Label-free prediction of three-dimensional fluorescence images from transmitted light microscopy},
-year = {2018},
-doi = {10.1101/289504},
-publisher = {Cold Spring Harbor Laboratory},
-URL = {https://www.biorxiv.org/content/early/2018/03/28/289504},
-eprint = {https://www.biorxiv.org/content/early/2018/03/28/289504.full.pdf},
-journal = {bioRxiv}
+@article{Ounkomol2018,
+  author = {Chawin Ounkomol and Sharmishtaa Seshamani and Mary M. Maleckar and Forrest Collman and Gregory R. Johnson},
+  title = {Label-free prediction of three-dimensional fluorescence images from transmitted-light microscopy},
+  journal = {Nature Methods}
+  doi = {10.1038/s41592-018-0111-2},
+  url = {https://doi.org/10.1038/s41592-018-0111-2},
+  year  = {2018},
+  month = {sep},
+  publisher = {Springer Nature America,  Inc},
+  volume = {15},
+  number = {11},
+  pages = {917--920},
+}
 ```
 
 ## Contact
 Gregory Johnson  
 E-mail: <gregj@alleninstitute.org>
 
 ## Allen Institute Software License
-This software license is the 2-clause BSD license plus clause a third clause that prohibits redistribution for commercial purposes without further permission.  
-Copyright © 2018. Allen Institute.  All rights reserved.  
+This software license is the 2-clause BSD license plus clause a third clause that prohibits redistribution and use for commercial purposes without further permission.   
+Copyright © 2018. Allen Institute.  All rights reserved.
 
-Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met:  
+Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met:
 1. Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer.  
 2. Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution.  
-3. Redistributions for commercial purposes are not permitted without the Allen Institute’s written permission. For purposes of this license, commercial purposes is the incorporation of the Allen Institute's software into anything for which you will charge fees or other compensation. Contact terms@alleninstitute.org for commercial licensing opportunities.  
+3. Redistributions and use for commercial purposes are not permitted without the Allen Institute’s written permission. For purposes of this license, commercial purposes are the incorporation of the Allen Institute's software into anything for which you will charge fees or other compensation or use of the software to perform a commercial service for a third party. Contact terms@alleninstitute.org for commercial licensing opportunities.  
 
 THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

scripts/paper/download_all_data.sh

@@ -1,6 +1,6 @@
 mkdir ./data
 
-declare -a arr=("beta_actin" "myosin_iib" "membrane_caax_63x" "desmoplakin" "sec61_beta", "st6gal1", "fibrillarin", "lamin_b1", "dic_lamin_b1" "alpha_tubulin" "tom20" "zo1" "timelapse_wt2_s2")
+declare -a arr=("beta_actin" "myosin_iib" "membrane_caax_63x" "desmoplakin" "sec61_beta" "st6gal1" "fibrillarin" "lamin_b1" "dic_lamin_b1" "alpha_tubulin" "tom20" "zo1" "timelapse_wt2_s2")
 
 for i in "${arr[@]}"
 do