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<!DOCTYPE html>
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<meta name="twitter:title" content="Proofreading" />
<meta
name="twitter:description"
content="## Registering To Proofread with CAVE1. **Apply for a CAVE account** by submitting [this form](https://forms.gle/tpbndoL1J6xB47KQ9). We will respond to your..."
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<!-- Logo and title -->
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Fish1 Release
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</header>
<div class="content">
<article class="feature-image">
<header
id="main"
style="background-image: url('/assets/img/fish1_banner.png')"
>
<div class="title-padder">
<h1 id="Proofreading" class="title">Proofreading</h1>
</div>
</header>
<section class="post-content">
<link rel="stylesheet" href="/assets/css/common.css" />
<h2 id="registering-to-proofread-with-cave">
Registering To Proofread with CAVE
</h2>
<ol>
<li>
<strong>Apply for a CAVE account</strong> by submitting
<a href="https://forms.gle/tpbndoL1J6xB47KQ9">this form</a>. We
will respond to your application within 24h.
</li>
<li>
After you’ve been approved, open one of the links above and
<strong
>click the Login button at the bottom of the neuroglancer
page.</strong
>
You must use the same email address you provided through your
application’s Google form.
</li>
<li>Now, you are all set to start proofreading!</li>
</ol>
<link rel="stylesheet" href="/assets/css/proofreading.css" />
<h2 id="proofreading-overview">Proofreading Overview</h2>
<p>
Proofreading is done in Neuroglancer, which you need to access
through a special link:
</p>
<p>Currently, we support proofreading for two datasets:</p>
<ol>
<li>
<p>
<a
href="https://ngl.brain-wire.org/#!middleauth+https://global.brain-wire-test.org/nglstate/api/v1/5668883604176896", target="_blank"
>Test dataset</a
>
</p>
<p>
The test dataset is a previous version of agglomeration for the
Fish1 and serves as a sandbox to test proofreading. The purpose
of this test dataset is for you to get familiar with the
proofreading process. You can just play around with it, and
don’t worry if your proofreading edits are correct or not. You
can access the test dataset through the link in the heading.
</p>
</li>
<li>
<p>
<a
href="https://ngl.brain-wire.org/#!middleauth+https://global.brain-wire-test.org/nglstate/api/v1/5702104035360768", target="_blank"
>The full dataset</a
>
</p>
<p>
The full dataset allows users to proofread the whole Fish1
volume.
<strong
>Only make proofreading edits if you are sure that those are
correct</strong
>. Eventually, changes in this dataset will contribute to
improved segmentation.
</p>
</li>
<li>
<p>
<a href="./tutorials.html">Tutorials</a> on
programmatically interacting with CAVE.
</p>
</li>
<li>
<p>
Proofreading
<a
href="https://www.youtube.com/playlist?list=PLM5M02VPpcOpvThgZSte-0EgLDt-MN5wL", target="_blank"
>Video Tutorials</a
>
on YouTube.
</p>
</li>
</ol>
<h2 id="making-proofreading-edits">Making Proofreading Edits</h2>
<p>
This is a detailed description of how to make proofreading edits.
</p>
<ol>
<li>
<p>
<strong>Setting shortcuts for edit commands</strong><br />
The link above has shortcuts for merge and cut operations
already defined.
</p>
<div class="language-plaintext highlighter-rouge">
<div class="highlight">
<pre class="highlight"><code> Shift + A → Merge
Shift + C → Cut
</code></pre>
</div>
</div>
<p>
If you want to change those shortcuts, you can bind new keys. In
the Graph tab, Click & hold the mouse over the Merge or
Multicut field. Next, hit the key you want to bind to the
operation. The letter next to the field will update if the new
shortcut was set successfully.
</p>
</li>
<li>
<p>
<strong>Merging two segments (Correct Split Errors)</strong
><br />
</p>
<p>
You can merge multiple segments at once. A single bulk merge can
merge up to 10 segments.
</p>
<ol>
<li>Select the segments you want to merge.</li>
<li>
Press
<code class="language-plaintext highlighter-rouge">M</code> on
your keyboard. This will bring up the merge menu:
<img
src="/assets/img/proofreading/proofreading_merging_image1.png"
alt=""
/>
</li>
<li>
<code class="language-plaintext highlighter-rouge"
>Control + Click</code
>
segment 1 (either in the 2D images or 3D meshes). You will see
a red line moving with your cursor.
<code class="language-plaintext highlighter-rouge"
>Control + Click</code
>
segment 2. You will see the red line connecting the two
segments. If done successfully, both segments will appear in
the merge menu.
<img
src="/assets/img/proofreading/proofreading_merging_image2.png"
alt=""
/>
</li>
<li>
This process can be repeated up to 10 times before submitting
the merge request.
<img
src="/assets/img/proofreading/proofreading_merging_image3.png"
alt=""
/>
</li>
<li>
Click <em>Submit</em> to merge previously selected segments.
If successful, the merged segments are rendered in the same
color.
<img
src="/assets/img/proofreading/proofreading_merging_image4.png"
alt=""
/>
</li>
<li>
If you have enabled auto-submit, the request will be sent
automatically after selecting each segment pair.
</li>
<li>
You can click <em>Clear</em> to cancel all your selections or
cancel a selection one by one using the <em>Trash</em> icon.
</li>
</ol>
</li>
<li>
<p>
<strong>Cut a segment in two (Correcting Merge Errors)</strong
><br />
</p>
<ol>
<li>
Go to the Graph Tab in the neuroglancer settings. In the above
link, the merge feature is bound to the C key. Make sure you
are in the Graph Tab and not (!) in the Seg. Tab.
</li>
<li>
Click
<code class="language-plaintext highlighter-rouge">C</code> to
open the cutting menu.
<img src="/assets/img/proofreading/image3.png" alt="" />
</li>
<li>
In the 3D view, place points around the region you want to
split on mesh 1. To place points hold
<code class="language-plaintext highlighter-rouge"
>Shift + Control</code
>
while you click on a mesh.
</li>
<li>
After you placed points on mesh 1, click Swap before you place
points on mesh 2
</li>
<li>
After you place points on both sides of the desired cut, it
should look similar to this
<blockquote>
<p>
Note: Usually placing ~3 points per side is enough.
<img src="/assets/img/proofreading/image4.png" alt="" />
</p>
</blockquote>
</li>
<li>
Click <em>Submit</em> to perform the cut. After a few seconds,
you should see both sides of the cut in separate colors. After
reloading neuroglancer, the meshes will update.
</li>
</ol>
</li>
</ol>
<!-- <h2 id="current-limitations-and-known-issues">
Current limitations and known issues
</h2>
<p>
Proofreading through the PyChunkedGraph has only been added recently
to the main neuroglancer branch (the one used here). This is a
different version of neuroglancer than what is used for FlyWire. The
Seung Lab is working on moving and improving all features to the
main neuroglancer branch; expect changes and improvements. Please
report bugs.
</p> -->
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