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<!DOCTYPE html>
<html class="no-js" lang="en">
<head>
<title>Brain Image Library: Data Submission Best Practices</title>
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<h2>Data Submission Best Practices</H2>
<p>This document outlines a few recommended best practices to structure your data uploads
to the Brain Image Library. If you have questions on how to structure
your data that is not answered here, please contact the help desk
([email protected]).</p>
<H3> General Practices</H3>
<H4>Perform general file cleanup after data transfer</H4>
Be aware that there may be operating system created hidden files transferred
along with your data that should be removed from the BIL landing-zone directory
prior to making your data public. These files may include:
<blockquote>
<ul>
<li><b>.DS_Store</b> -- An Apple macOS file
(for more information see: <a href="https://en.wikipedia.org/wiki/.DS_Store">https://en.wikipedia.org/wiki/.DS_Store</a>)</li>
<li><b>Thumbs.db</b> -- A Microsoft Windows file
(for more information see <a href="https://en.wikipedia.org/wiki/Windows_thumbnail_cache">https://en.wikipedia.org/wiki/Windows_thumbnail_cache</a>)</li>
</ul></blockquote>
<H4>Avoid problematic special characters:</h4>
Use characters that are generally safe in your filenames. Avoid special characters in filenames that can be problematic on a unix/linux system.
<blockquote>
<p><b>Characters that are generally safe to include in filenames:</b>
<ul>
<li>Underscore <span class="badge bg-success text-light"><u> </u></span></li>
<li>Dash <span class="badge bg-success text-light">-</span> </li>
<li>Period <span class="badge bg-success text-light">.</span> </li>
<li>Lower-case letters <span class="badge bg-success text-light">a-z</span></li>
<li>Upper-case letters <span class="badge bg-success text-light">A-Z</span></li>
<li>Numbers <span class="badge bg-success text-light">0-9</span></li>
</ul>
<b>Special characters that can be problematic:</b>
<ul>
<li>Space <span class="badge badge-warning text-muted"> </span></li>
<li>Ampersand <span class="badge badge-warning text-muted">&</span> </li>
<li>Slash <span class="badge badge-warning text-muted">/</span> </li>
<li>Vertical bar <span class="badge badge-warning text-muted">|</span> </li>
<li>Colon <span class="badge badge-warning text-muted">:</span> </li>
<li>Semicolon <span class="badge badge-warning text-muted">;</span> </li>
<li>Greater-than <span class="badge badge-warning text-muted">></span> </li>
<li>Less-than <span class="badge badge-warning text-muted"><</span> </li>
<li>Question <span class="badge badge-warning text-muted">?</span> </li>
<li>Asterisk <span class="badge badge-warning text-muted">*</span></li>
</ul>
</p>
</blockquote>
<H4>Only place subdirectories in the root of the landing-zone</h4>
<p>The submission portal will create a landing-zone directory for you to upload your data to.
Please do not place files in this root directory, but rather create one or more subdirectories
here for each dataset that you are uploading. Then upload each dataset under the
subdirectories that you have created. Note that the complete path to the directory that you
have created should be entered in the metadata spreadsheet along with the associated metadata
for each dataset. </p>
<H3>Modality-Specific Recommendations</H3>
<p>Below are modality-specific recommendtions. If your exact data type is not listed,
you can model your submission with the closest type or contact [email protected] for more information. </p>
<h4>Whole brain datasets containing only lower-level data</h4>
<p>To tie metadata to an image dataset (a stack of z-planes), each image dataset must be
uploaded in a separate subdirectory. For example, if you had an experiment containing
5 mouse datasets (with sample names of mouse1, mouse2, mouse3, mouse4, mouse5) that
you wanted to to include as a single submission collection, you would create 5 subdirectories
in the landing zone for the submission collection, one for each mouse dataset. e.g:
</p>
<pre>
/bil/lz/testuser/abcdef0123456789/mouse1
/bil/lz/testuser/abcdef0123456789/mouse2
/bil/lz/testuser/abcdef0123456789/mouse3
/bil/lz/testuser/abcdef0123456789/mouse4
/bil/lz/testuser/abcdef0123456789/mouse5
</pre>
<p>If you have additional (non BIL required) metadata that you want to include with each dataset, place
it in a subdirectory
called <i>extras</i> inside each subdirectory:</p>
<pre>
/bil/lz/testuser/abcdef0123456789/mouse1/extras
</pre>
<h4>Whole brain data containing a mix of lower-level and higher level data</h4>
<p> If the dataset contains a mix of lower-level and higher level data, note that
in our system, each level of data is considered a unique dataset. We recommend that you
follow the general advice above for <i>Whole brain datasets containing only lower-level
data</i>.
For example, if you had an experiment containing
5 mouse datasets (with sample names of mouse1, mouse2, mouse3, mouse4, mouse5) that
you wanted to to include as a single submission collection, you would create 5 subdirectories
in the landing zone for the submission collection, one for each mouse dataset. e.g:
</p>
<pre>
/bil/lz/testuser/abcdef0123456789/mouse1
/bil/lz/testuser/abcdef0123456789/mouse2
/bil/lz/testuser/abcdef0123456789/mouse3
/bil/lz/testuser/abcdef0123456789/mouse4
/bil/lz/testuser/abcdef0123456789/mouse5
</pre>
<p> Next, create subdirectories that indicate the level of processing done on the data.
Recommended subdirectory names to use would include: <i>raw</i>, <i>unstitched</i>, <i>stitched</i>, <i>aligned</i>, <i>tracings</i>, <i>masks</i>. If multiple-resolutions
are provided, use names indicative of the resolution (e.g. <i>10x</i>, <i>30x</i> or some other descriptive lable such as <i>40micron</i>). Also, create a readme.txt file in a <b>required</b>
<i>extras</i> subdirectory that describes the content of each subdirectory. For example:
<pre>
/bil/lz/testuser/abcdef0123456789/mouse1/stitched
/bil/lz/testuser/abcdef0123456789/mouse1/aligned
/bil/lz/testuser/abcdef0123456789/mouse1/tracings
/bil/lz/testuser/abcdef0123456789/mouse1/extras/readme.txt
</pre>
<p>Feel free to add additional (non BIL required) metadata that you want to include with each dataset
in the extras subdirectories. </p>
<p> </p>
<h4>Whole brain datasets containing only higher-level data</h4>
<p>It is not unusual to make lower-level image data available before the higher-level
analysis is complete. When you are ready to submit this data, you would need to create
a new submission. In this case, use the same sample name as the prior BIL submission and
a subdirectory to indicate the level of procesing (see recommended names above under
<i>Whole brain data containing a mix of lower-level and higher level data</i>.
For example, If SWC tracing files were provided for the sample named "mouse1" at a later
date, you might create a directory like:
</p>
<pre>
/bil/lz/testuser/fef9236f6400b832/mouse1/tracings
</pre>
</p>
<p> </p>
<h4>Spatial transcriptomic datasets</h4>
<p>We recommend that spatial transcriptomic data contains both the raw and processed image
data as well as the processed csvs. Please submit your image data using the following directory structure: </p>
<pre>
/bil/lz/testuser/abcdef0123456789/mouse1/raw/mouse1_sample1
/bil/lz/testuser/abcdef0123456789/mouse1/raw/mouse1_sample2
/bil/lz/testuser/abcdef0123456789/mouse1/raw/mouse2_sample1
/bil/lz/testuser/abcdef0123456789/mouse1/raw/mouse2_sample2
/bil/lz/testuser/abcdef0123456789/mouse1/processed/mouse1_sample1
/bil/lz/testuser/abcdef0123456789/mouse1/processed/mouse1_sample2
/bil/lz/testuser/abcdef0123456789/mouse1/processed/mouse2_sample1
/bil/lz/testuser/abcdef0123456789/mouse1/processed/mouse2_sample2
</pre>
<p>Place your experiment-wide processed data as csv files in a subdirectory
called <i>processed</i>:</p>
<pre>
/bil/lz/testuser/abcdef0123456789/processed
</pre>
<p>If you have additional metadata that you want to include, place it in a subdirectory
called <i>extras</i> along with any other notes that you want to include about the data:</p>
<pre>
/bil/lz/testuser/abcdef0123456789/extras
</pre>
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