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lukasmueller merged 2 commits into from
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Images manual updates #5874

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Change image chapter names and add image upload info
bm743 Jan 30, 2026
f10e086
update bookdown docs
invalid-email-address Jan 30, 2026
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19 changes: 10 additions & 9 deletions docs/404.html
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<meta name="author" content="Breedbase team" />


<meta name="date" content="2026-01-08" />
<meta name="date" content="2026-01-30" />

<meta name="viewport" content="width=device-width, initial-scale=1" />
<meta name="apple-mobile-web-app-capable" content="yes" />
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<ul>
<li class="chapter" data-level="20.1" data-path="managing-observation-variables.html"><a href="managing-observation-variables.html#managing-observation-variables-with-traits-methods-and-scales"><i class="fa fa-check"></i><b>20.1</b> Managing Observation Variables with Traits, Methods, and Scales</a></li>
</ul></li>
<li class="chapter" data-level="21" data-path="managing-image-data.html"><a href="managing-image-data.html"><i class="fa fa-check"></i><b>21</b> Managing Image Data</a>
<li class="chapter" data-level="21" data-path="managing-drone-imagery.html"><a href="managing-drone-imagery.html"><i class="fa fa-check"></i><b>21</b> Managing Drone Imagery</a>
<ul>
<li class="chapter" data-level="21.1" data-path="managing-image-data.html"><a href="managing-image-data.html#image-phenotyping-dashboard"><i class="fa fa-check"></i><b>21.1</b> Image-Phenotyping Dashboard</a></li>
<li class="chapter" data-level="21.2" data-path="managing-image-data.html"><a href="managing-image-data.html#image-input"><i class="fa fa-check"></i><b>21.2</b> Image Input</a></li>
<li class="chapter" data-level="21.3" data-path="managing-image-data.html"><a href="managing-image-data.html#standard-process"><i class="fa fa-check"></i><b>21.3</b> Standard Process</a></li>
<li class="chapter" data-level="21.4" data-path="managing-image-data.html"><a href="managing-image-data.html#ground-control-points"><i class="fa fa-check"></i><b>21.4</b> Ground Control Points</a></li>
<li class="chapter" data-level="21.1" data-path="managing-drone-imagery.html"><a href="managing-drone-imagery.html#image-phenotyping-dashboard"><i class="fa fa-check"></i><b>21.1</b> Image-Phenotyping Dashboard</a></li>
<li class="chapter" data-level="21.2" data-path="managing-drone-imagery.html"><a href="managing-drone-imagery.html#image-input"><i class="fa fa-check"></i><b>21.2</b> Image Input</a></li>
<li class="chapter" data-level="21.3" data-path="managing-drone-imagery.html"><a href="managing-drone-imagery.html#standard-process"><i class="fa fa-check"></i><b>21.3</b> Standard Process</a></li>
<li class="chapter" data-level="21.4" data-path="managing-drone-imagery.html"><a href="managing-drone-imagery.html#ground-control-points"><i class="fa fa-check"></i><b>21.4</b> Ground Control Points</a></li>
</ul></li>
<li class="chapter" data-level="22" data-path="managing-phenotypic-image-data.html"><a href="managing-phenotypic-image-data.html"><i class="fa fa-check"></i><b>22</b> Managing Phenotypic Image Data</a>
<li class="chapter" data-level="22" data-path="managing-images.html"><a href="managing-images.html"><i class="fa fa-check"></i><b>22</b> Managing Images</a>
<ul>
<li class="chapter" data-level="22.1" data-path="managing-phenotypic-image-data.html"><a href="managing-phenotypic-image-data.html#uploading-image-files"><i class="fa fa-check"></i><b>22.1</b> Uploading Image files</a></li>
<li class="chapter" data-level="22.2" data-path="managing-phenotypic-image-data.html"><a href="managing-phenotypic-image-data.html#uploading-images-directly-to-stocks"><i class="fa fa-check"></i><b>22.2</b> Uploading Images Directly to Stocks</a></li>
<li class="chapter" data-level="22.1" data-path="managing-images.html"><a href="managing-images.html#uploading-image-files"><i class="fa fa-check"></i><b>22.1</b> Uploading Image files</a></li>
<li class="chapter" data-level="22.2" data-path="managing-images.html"><a href="managing-images.html#uploading-images-directly-to-stocks"><i class="fa fa-check"></i><b>22.2</b> Uploading Images Directly to Stocks</a></li>
<li class="chapter" data-level="22.3" data-path="managing-images.html"><a href="managing-images.html#uploading-images-from-the-field-trial-and-image-analysis-pages"><i class="fa fa-check"></i><b>22.3</b> Uploading Images from the Field Trial and Image Analysis Pages</a></li>
</ul></li>
<li class="chapter" data-level="23" data-path="managing-vcf-data.html"><a href="managing-vcf-data.html"><i class="fa fa-check"></i><b>23</b> Managing VCF Data</a>
<ul>
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27 changes: 22 additions & 5 deletions docs/BreedbaseManual.tex
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\title{Breedbase User Manual}
\author{Breedbase team}
\date{2026-01-08}
\date{2026-01-30}

\begin{document}
\maketitle
Expand Down Expand Up @@ -2504,8 +2504,8 @@ \section{Managing Observation Variables with Traits, Methods, and Scales}\label{

Afterwards, you can use the newly created observation variable ontology term in your phenotyping.

\hypertarget{managing-image-data}{%
\chapter{Managing Image Data}\label{managing-image-data}}
\hypertarget{managing-drone-imagery}{%
\chapter{Managing Drone Imagery}\label{managing-drone-imagery}}

\hypertarget{image-phenotyping-dashboard}{%
\section{Image-Phenotyping Dashboard}\label{image-phenotyping-dashboard}}
Expand Down Expand Up @@ -2614,8 +2614,8 @@ \section{Ground Control Points}\label{ground-control-points}}

Ground control points can be saved after an imaging event has undergone the standard process on orhomosaics. Ground control points can then be used across imaging events on the same field experiment in order to automate the entire standard process.

\hypertarget{managing-phenotypic-image-data}{%
\chapter{Managing Phenotypic Image Data}\label{managing-phenotypic-image-data}}
\hypertarget{managing-images}{%
\chapter{Managing Images}\label{managing-images}}

\hypertarget{uploading-image-files}{%
\section{Uploading Image files}\label{uploading-image-files}}
Expand Down Expand Up @@ -2647,6 +2647,23 @@ \section{Uploading Images Directly to Stocks}\label{uploading-images-directly-to

\begin{center}\includegraphics[width=0.95\linewidth]{assets/images/stock_add_image} \end{center}

\hypertarget{uploading-images-from-the-field-trial-and-image-analysis-pages}{%
\section{Uploading Images from the Field Trial and Image Analysis Pages}\label{uploading-images-from-the-field-trial-and-image-analysis-pages}}

Another way to upload images is through the field trial details page. Navigate to a field trial details page and open the ``Images'' section.

\begin{center}\includegraphics[width=0.95\linewidth]{assets/images/field_trial_images} \end{center}

Then click the ``Add New Image'' button to open the image upload dialog, where images can be uploaded in the same formats as described previously.

\begin{center}\includegraphics[width=0.95\linewidth]{assets/images/add_new_image_trial} \end{center}

To upload images from the Image Analysis page, click on ``Image Analysis'' under the ``Analyze'' menu. Then click the ``Upload New Images'' button on this page.

\begin{center}\includegraphics[width=0.95\linewidth]{assets/images/image_analysis_add_image} \end{center}

This will open the same image upload dialog.

\hypertarget{managing-vcf-data}{%
\chapter{Managing VCF Data}\label{managing-vcf-data}}

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19 changes: 10 additions & 9 deletions docs/Using-Field-Book-with-BreedBase.html
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<meta name="author" content="Breedbase team" />


<meta name="date" content="2026-01-08" />
<meta name="date" content="2026-01-30" />

<meta name="viewport" content="width=device-width, initial-scale=1" />
<meta name="apple-mobile-web-app-capable" content="yes" />
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<ul>
<li class="chapter" data-level="20.1" data-path="managing-observation-variables.html"><a href="managing-observation-variables.html#managing-observation-variables-with-traits-methods-and-scales"><i class="fa fa-check"></i><b>20.1</b> Managing Observation Variables with Traits, Methods, and Scales</a></li>
</ul></li>
<li class="chapter" data-level="21" data-path="managing-image-data.html"><a href="managing-image-data.html"><i class="fa fa-check"></i><b>21</b> Managing Image Data</a>
<li class="chapter" data-level="21" data-path="managing-drone-imagery.html"><a href="managing-drone-imagery.html"><i class="fa fa-check"></i><b>21</b> Managing Drone Imagery</a>
<ul>
<li class="chapter" data-level="21.1" data-path="managing-image-data.html"><a href="managing-image-data.html#image-phenotyping-dashboard"><i class="fa fa-check"></i><b>21.1</b> Image-Phenotyping Dashboard</a></li>
<li class="chapter" data-level="21.2" data-path="managing-image-data.html"><a href="managing-image-data.html#image-input"><i class="fa fa-check"></i><b>21.2</b> Image Input</a></li>
<li class="chapter" data-level="21.3" data-path="managing-image-data.html"><a href="managing-image-data.html#standard-process"><i class="fa fa-check"></i><b>21.3</b> Standard Process</a></li>
<li class="chapter" data-level="21.4" data-path="managing-image-data.html"><a href="managing-image-data.html#ground-control-points"><i class="fa fa-check"></i><b>21.4</b> Ground Control Points</a></li>
<li class="chapter" data-level="21.1" data-path="managing-drone-imagery.html"><a href="managing-drone-imagery.html#image-phenotyping-dashboard"><i class="fa fa-check"></i><b>21.1</b> Image-Phenotyping Dashboard</a></li>
<li class="chapter" data-level="21.2" data-path="managing-drone-imagery.html"><a href="managing-drone-imagery.html#image-input"><i class="fa fa-check"></i><b>21.2</b> Image Input</a></li>
<li class="chapter" data-level="21.3" data-path="managing-drone-imagery.html"><a href="managing-drone-imagery.html#standard-process"><i class="fa fa-check"></i><b>21.3</b> Standard Process</a></li>
<li class="chapter" data-level="21.4" data-path="managing-drone-imagery.html"><a href="managing-drone-imagery.html#ground-control-points"><i class="fa fa-check"></i><b>21.4</b> Ground Control Points</a></li>
</ul></li>
<li class="chapter" data-level="22" data-path="managing-phenotypic-image-data.html"><a href="managing-phenotypic-image-data.html"><i class="fa fa-check"></i><b>22</b> Managing Phenotypic Image Data</a>
<li class="chapter" data-level="22" data-path="managing-images.html"><a href="managing-images.html"><i class="fa fa-check"></i><b>22</b> Managing Images</a>
<ul>
<li class="chapter" data-level="22.1" data-path="managing-phenotypic-image-data.html"><a href="managing-phenotypic-image-data.html#uploading-image-files"><i class="fa fa-check"></i><b>22.1</b> Uploading Image files</a></li>
<li class="chapter" data-level="22.2" data-path="managing-phenotypic-image-data.html"><a href="managing-phenotypic-image-data.html#uploading-images-directly-to-stocks"><i class="fa fa-check"></i><b>22.2</b> Uploading Images Directly to Stocks</a></li>
<li class="chapter" data-level="22.1" data-path="managing-images.html"><a href="managing-images.html#uploading-image-files"><i class="fa fa-check"></i><b>22.1</b> Uploading Image files</a></li>
<li class="chapter" data-level="22.2" data-path="managing-images.html"><a href="managing-images.html#uploading-images-directly-to-stocks"><i class="fa fa-check"></i><b>22.2</b> Uploading Images Directly to Stocks</a></li>
<li class="chapter" data-level="22.3" data-path="managing-images.html"><a href="managing-images.html#uploading-images-from-the-field-trial-and-image-analysis-pages"><i class="fa fa-check"></i><b>22.3</b> Uploading Images from the Field Trial and Image Analysis Pages</a></li>
</ul></li>
<li class="chapter" data-level="23" data-path="managing-vcf-data.html"><a href="managing-vcf-data.html"><i class="fa fa-check"></i><b>23</b> Managing VCF Data</a>
<ul>
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19 changes: 10 additions & 9 deletions docs/basic-website-usage.html
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<meta name="author" content="Breedbase team" />


<meta name="date" content="2026-01-08" />
<meta name="date" content="2026-01-30" />

<meta name="viewport" content="width=device-width, initial-scale=1" />
<meta name="apple-mobile-web-app-capable" content="yes" />
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<ul>
<li class="chapter" data-level="20.1" data-path="managing-observation-variables.html"><a href="managing-observation-variables.html#managing-observation-variables-with-traits-methods-and-scales"><i class="fa fa-check"></i><b>20.1</b> Managing Observation Variables with Traits, Methods, and Scales</a></li>
</ul></li>
<li class="chapter" data-level="21" data-path="managing-image-data.html"><a href="managing-image-data.html"><i class="fa fa-check"></i><b>21</b> Managing Image Data</a>
<li class="chapter" data-level="21" data-path="managing-drone-imagery.html"><a href="managing-drone-imagery.html"><i class="fa fa-check"></i><b>21</b> Managing Drone Imagery</a>
<ul>
<li class="chapter" data-level="21.1" data-path="managing-image-data.html"><a href="managing-image-data.html#image-phenotyping-dashboard"><i class="fa fa-check"></i><b>21.1</b> Image-Phenotyping Dashboard</a></li>
<li class="chapter" data-level="21.2" data-path="managing-image-data.html"><a href="managing-image-data.html#image-input"><i class="fa fa-check"></i><b>21.2</b> Image Input</a></li>
<li class="chapter" data-level="21.3" data-path="managing-image-data.html"><a href="managing-image-data.html#standard-process"><i class="fa fa-check"></i><b>21.3</b> Standard Process</a></li>
<li class="chapter" data-level="21.4" data-path="managing-image-data.html"><a href="managing-image-data.html#ground-control-points"><i class="fa fa-check"></i><b>21.4</b> Ground Control Points</a></li>
<li class="chapter" data-level="21.1" data-path="managing-drone-imagery.html"><a href="managing-drone-imagery.html#image-phenotyping-dashboard"><i class="fa fa-check"></i><b>21.1</b> Image-Phenotyping Dashboard</a></li>
<li class="chapter" data-level="21.2" data-path="managing-drone-imagery.html"><a href="managing-drone-imagery.html#image-input"><i class="fa fa-check"></i><b>21.2</b> Image Input</a></li>
<li class="chapter" data-level="21.3" data-path="managing-drone-imagery.html"><a href="managing-drone-imagery.html#standard-process"><i class="fa fa-check"></i><b>21.3</b> Standard Process</a></li>
<li class="chapter" data-level="21.4" data-path="managing-drone-imagery.html"><a href="managing-drone-imagery.html#ground-control-points"><i class="fa fa-check"></i><b>21.4</b> Ground Control Points</a></li>
</ul></li>
<li class="chapter" data-level="22" data-path="managing-phenotypic-image-data.html"><a href="managing-phenotypic-image-data.html"><i class="fa fa-check"></i><b>22</b> Managing Phenotypic Image Data</a>
<li class="chapter" data-level="22" data-path="managing-images.html"><a href="managing-images.html"><i class="fa fa-check"></i><b>22</b> Managing Images</a>
<ul>
<li class="chapter" data-level="22.1" data-path="managing-phenotypic-image-data.html"><a href="managing-phenotypic-image-data.html#uploading-image-files"><i class="fa fa-check"></i><b>22.1</b> Uploading Image files</a></li>
<li class="chapter" data-level="22.2" data-path="managing-phenotypic-image-data.html"><a href="managing-phenotypic-image-data.html#uploading-images-directly-to-stocks"><i class="fa fa-check"></i><b>22.2</b> Uploading Images Directly to Stocks</a></li>
<li class="chapter" data-level="22.1" data-path="managing-images.html"><a href="managing-images.html#uploading-image-files"><i class="fa fa-check"></i><b>22.1</b> Uploading Image files</a></li>
<li class="chapter" data-level="22.2" data-path="managing-images.html"><a href="managing-images.html#uploading-images-directly-to-stocks"><i class="fa fa-check"></i><b>22.2</b> Uploading Images Directly to Stocks</a></li>
<li class="chapter" data-level="22.3" data-path="managing-images.html"><a href="managing-images.html#uploading-images-from-the-field-trial-and-image-analysis-pages"><i class="fa fa-check"></i><b>22.3</b> Uploading Images from the Field Trial and Image Analysis Pages</a></li>
</ul></li>
<li class="chapter" data-level="23" data-path="managing-vcf-data.html"><a href="managing-vcf-data.html"><i class="fa fa-check"></i><b>23</b> Managing VCF Data</a>
<ul>
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<meta name="author" content="Breedbase team" />


<meta name="date" content="2026-01-08" />
<meta name="date" content="2026-01-30" />

<meta name="viewport" content="width=device-width, initial-scale=1" />
<meta name="apple-mobile-web-app-capable" content="yes" />
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<ul>
<li class="chapter" data-level="20.1" data-path="managing-observation-variables.html"><a href="managing-observation-variables.html#managing-observation-variables-with-traits-methods-and-scales"><i class="fa fa-check"></i><b>20.1</b> Managing Observation Variables with Traits, Methods, and Scales</a></li>
</ul></li>
<li class="chapter" data-level="21" data-path="managing-image-data.html"><a href="managing-image-data.html"><i class="fa fa-check"></i><b>21</b> Managing Image Data</a>
<li class="chapter" data-level="21" data-path="managing-drone-imagery.html"><a href="managing-drone-imagery.html"><i class="fa fa-check"></i><b>21</b> Managing Drone Imagery</a>
<ul>
<li class="chapter" data-level="21.1" data-path="managing-image-data.html"><a href="managing-image-data.html#image-phenotyping-dashboard"><i class="fa fa-check"></i><b>21.1</b> Image-Phenotyping Dashboard</a></li>
<li class="chapter" data-level="21.2" data-path="managing-image-data.html"><a href="managing-image-data.html#image-input"><i class="fa fa-check"></i><b>21.2</b> Image Input</a></li>
<li class="chapter" data-level="21.3" data-path="managing-image-data.html"><a href="managing-image-data.html#standard-process"><i class="fa fa-check"></i><b>21.3</b> Standard Process</a></li>
<li class="chapter" data-level="21.4" data-path="managing-image-data.html"><a href="managing-image-data.html#ground-control-points"><i class="fa fa-check"></i><b>21.4</b> Ground Control Points</a></li>
<li class="chapter" data-level="21.1" data-path="managing-drone-imagery.html"><a href="managing-drone-imagery.html#image-phenotyping-dashboard"><i class="fa fa-check"></i><b>21.1</b> Image-Phenotyping Dashboard</a></li>
<li class="chapter" data-level="21.2" data-path="managing-drone-imagery.html"><a href="managing-drone-imagery.html#image-input"><i class="fa fa-check"></i><b>21.2</b> Image Input</a></li>
<li class="chapter" data-level="21.3" data-path="managing-drone-imagery.html"><a href="managing-drone-imagery.html#standard-process"><i class="fa fa-check"></i><b>21.3</b> Standard Process</a></li>
<li class="chapter" data-level="21.4" data-path="managing-drone-imagery.html"><a href="managing-drone-imagery.html#ground-control-points"><i class="fa fa-check"></i><b>21.4</b> Ground Control Points</a></li>
</ul></li>
<li class="chapter" data-level="22" data-path="managing-phenotypic-image-data.html"><a href="managing-phenotypic-image-data.html"><i class="fa fa-check"></i><b>22</b> Managing Phenotypic Image Data</a>
<li class="chapter" data-level="22" data-path="managing-images.html"><a href="managing-images.html"><i class="fa fa-check"></i><b>22</b> Managing Images</a>
<ul>
<li class="chapter" data-level="22.1" data-path="managing-phenotypic-image-data.html"><a href="managing-phenotypic-image-data.html#uploading-image-files"><i class="fa fa-check"></i><b>22.1</b> Uploading Image files</a></li>
<li class="chapter" data-level="22.2" data-path="managing-phenotypic-image-data.html"><a href="managing-phenotypic-image-data.html#uploading-images-directly-to-stocks"><i class="fa fa-check"></i><b>22.2</b> Uploading Images Directly to Stocks</a></li>
<li class="chapter" data-level="22.1" data-path="managing-images.html"><a href="managing-images.html#uploading-image-files"><i class="fa fa-check"></i><b>22.1</b> Uploading Image files</a></li>
<li class="chapter" data-level="22.2" data-path="managing-images.html"><a href="managing-images.html#uploading-images-directly-to-stocks"><i class="fa fa-check"></i><b>22.2</b> Uploading Images Directly to Stocks</a></li>
<li class="chapter" data-level="22.3" data-path="managing-images.html"><a href="managing-images.html#uploading-images-from-the-field-trial-and-image-analysis-pages"><i class="fa fa-check"></i><b>22.3</b> Uploading Images from the Field Trial and Image Analysis Pages</a></li>
</ul></li>
<li class="chapter" data-level="23" data-path="managing-vcf-data.html"><a href="managing-vcf-data.html"><i class="fa fa-check"></i><b>23</b> Managing VCF Data</a>
<ul>
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