Skip to content

Commit

Permalink
updated publications etc
Browse files Browse the repository at this point in the history
  • Loading branch information
@krokicki
krokicki committed Nov 26, 2024
1 parent 29d43d8 commit 2bb750a
Show file tree
Hide file tree
Showing 5 changed files with 64 additions and 23 deletions.
12 changes: 12 additions & 0 deletions assets/scss/_styles_project.scss
View file
Original file line number Diff line number Diff line change
Expand Up @@ -21,4 +21,16 @@
.aligncenter {
display: block;
margin: 0 auto;
}

.publication-list {
list-style-type: none;
}

.publication-list li {
margin-bottom: 10pt;
}

.text-horta-secondary3 {
color: $horta-secondary3;
}
4 changes: 3 additions & 1 deletion assets/scss/_variables_project_after_bs.scss
View file
Original file line number Diff line number Diff line change
Expand Up @@ -2,12 +2,14 @@ $horta-primary: #3e406a;
$horta-dark: #2a2c4c;
$horta-secondary: #bfac4f;
$horta-secondary2: #f6e793;
$horta-secondary3: #b3b5df;

$custom-colors: (
'horta-primary': $horta-primary,
'horta-dark': $horta-dark,
'horta-secondary': $horta-secondary,
'horta-secondary2': $horta-secondary2
'horta-secondary2': $horta-secondary2,
'horta-secondary3': $horta-secondary3
);

$theme-colors: map-merge($theme-colors, $custom-colors);
21 changes: 8 additions & 13 deletions content/_index.html
View file
Original file line number Diff line number Diff line change
Expand Up @@ -67,27 +67,22 @@ <h1 class="text-center pb-4">The Next-Generation Platform for Neuron Tracing</h1
<a href="screenshot-horta.png"><img src="screenshot-horta.png" class="img-fluid" style="float: left; width: 800px; padding: 0pt 20pt 20pt 0pt;"></a>
</p>

<p>
<h2>Features</h2>
<p class="text-horta-secondary3">
HortaCloud combines state-of-the-art volumetric visualization, advanced features for 3D neuronal annotation, and real-time multi-user collaboration

with a set of enterprise-grade backend microservices for moving and processing large amounts of data rapidly and securely.

Users can load multi-terabyte image volumes with up to three signal channels, and visualize them in 3D with multiscale volume rendering.

An optimized workflow allows annotators to efficiently trace long range projection neurons in light microscopy data, including easy merging/splitting of skeletal reconstructions.

Collaboration features allow a team of annotators to work together to annotate different neurons in a single volume, or build consensus by annotating the same neurons.
</p>

<p>
<p class="text-horta-secondary3">
Horta also provides other useful features, including:
<div style="display: inline-block">
<ul class="padding-left: 20pt;">
<li class="">Movie scripting and rendering</li>
<li class="">Import/export in SWC format</li>
<li class="">Text annotations</li>
<li class="">Color adjustments</li>
<li class="">Shared workspaces</li>
<li class="text-horta-secondary3">Movie scripting and rendering</li>
<li class="text-horta-secondary3">Import/export in SWC format</li>
<li class="text-horta-secondary3">Shared workspaces</li>
</ul>
</div>
</p>
Expand All @@ -97,15 +92,15 @@ <h1 class="text-center pb-4">The Next-Generation Platform for Neuron Tracing</h1
</p>

<h2>Software architecture</h2>
<p>
<p class="text-horta-secondary3">
This software is built on the Janelia Workstation platform, leveraging Java NetBeans to provide modularity and extensibility.
The backend consists of Java-based microservices that scale to handle large volumes of data.
Metadata is stored in MongoDB and real-time event handling is implemented using RabbitMQ.

We deploy both the client and backend services to the AWS Cloud, leveraging AWS AppStream to process the 3D rendering and virtualize the desktop infrastructure.
</p>

<p>
<p class="text-horta-secondary3">
Image data is stored on AWS S3, and we provide many open data sets on AWS Open Data registry that are immediately accessible in the application.
</p>

Expand Down
43 changes: 36 additions & 7 deletions content/publications.html
View file
Original file line number Diff line number Diff line change
Expand Up @@ -11,15 +11,44 @@

<h2>Publications</h2>

<p>
<p class="text-horta-secondary3" style="margin-top: 18pt;">
If you use HortaCloud in your work, please cite the following publications:
</p>

<li>
Winnubst J, Bas E, Ferreira TA, Wu Z, Economo MN, Edson P, Arthur BJ, Bruns C, Rokicki K, Schauder D, Olbris DJ, Murphy SD, Ackerman DG, Arshadi C, Baldwin P, Blake R, Elsayed A, Hasan M, Ramirez D, Dos Santos B,
Weldon M, Zafar A, Dudman JT, Gerfen CR, Hantman AW, Korff W, Sternson SM, Spruston N, Svoboda K, Chandrashekar J.
<u>Reconstruction of 1,000 Projection Neurons Reveals New Cell Types and Organization of Long-Range Connectivity in the Mouse Brain</u>. Cell. 2019 Sep 19;179(1):268-281.e13.
doi: <a href="https://doi.org/10.1016/j.cell.2019.07.042">10.1016/j.cell.2019.07.042</a>
</li>
<ul class="publication-list">
<li>
HortaCloud paper (in prep)
</li>
</ul>

<p class="text-horta-secondary3" style="margin-top: 18pt;">
HortaCloud has been featured in the following publications:
</p>

<ul class="publication-list">
<!--
<li>(morphoFISH citation) (To be added)</li>
<li>Emily Tenshaw, Mary Lay, Alyssa Stark, Monet Weldon, Cameron Arshadi, Ahmad Elsayed, Daniel Ramirez, Bruno Dos Santos, Amina Zafar, Mashtura Hasan,
Regina Blake, Jayaram Chandrashekar, Tiago A Ferreira . Reconstructing Complete Neurons in Whole Brains Using HortaCloud.
Protocol exchange https://protocols.io/view/reconstructing-complete-neurons-in-whole-brains-us-c9vkz64w
</li>
-->

<li>
Winnubst J, Bas E, Ferreira TA, Wu Z, Economo MN, Edson P, Arthur BJ, Bruns C, Rokicki K, Schauder D, Olbris DJ, Murphy SD, Ackerman DG, Arshadi C, Baldwin P, Blake R, Elsayed A, Hasan M, Ramirez D, Dos Santos B,
Weldon M, Zafar A, Dudman JT, Gerfen CR, Hantman AW, Korff W, Sternson SM, Spruston N, Svoboda K, Chandrashekar J.
<u>Reconstruction of 1,000 Projection Neurons Reveals New Cell Types and Organization of Long-Range Connectivity in the Mouse Brain</u>. Cell. 2019 Sep 19;179(1):268-281.e13.
doi: <a href="https://doi.org/10.1016/j.cell.2019.07.042">10.1016/j.cell.2019.07.042</a>
</li>

<li>
Economo MN, Clack NG, Lavis LD, Gerfen CR, Svoboda K, Myers EW, Chandrashekar J. <u>A platform for brain-wide imaging and reconstruction of individual neurons</u>.
Elife. 2016 Jan 20;5:e10566. doi: <a href="https://doi.org/10.7554/eLife.10566">10.7554/eLife.10566</a>
</li>
</ul>




{{< /blocks/section >}}
7 changes: 5 additions & 2 deletions content/team.html
View file
Original file line number Diff line number Diff line change
Expand Up @@ -9,6 +9,11 @@

{{< blocks/section color="horta-dark" >}}

<div class="text-horta-secondary3" style="margin-bottom: 15pt; text-align: center;">
HortaCloud was primarily developed by Scientific Computing Software at Janelia Research Campus in collaboration with the Janelia MouseLight project team.
<br>
Contributors are listed in alphabetical order. Special thanks to Brie Yarbrough for creating the HortaCloud logo.
</div>

<h2 style="text-align: center;">Advisors</h2>

Expand Down Expand Up @@ -146,6 +151,4 @@ <h5 class="card-title">Rob Svirskas</h5>

</div>

<p style="text-align: center;">Special thanks to Brie Yarbrough for creating the HortaCloud logo.</p>

{{< /blocks/section >}}

0 comments on commit 2bb750a

Please sign in to comment.