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268 changes: 57 additions & 211 deletions topics/imaging/tutorials/voronoi-segmentation/tutorial.md
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layout: tutorial_hands_on

title: Voronoi Segmentation
zenodo_link: ''
zenodo_link: 'https://doi.org/10.5281/zenodo.5494629'
questions:
- How to use Galaxy for Voronoi Segmentation?
- How should images be prepared before applying Voronoi segmentation?
Expand Down Expand Up @@ -59,120 +59,106 @@ In Earth observation, Voronoi segmentation is used to analyze spatial patterns a
>
{: .agenda}

# Title for your first section
# Get data

Give some background about what the trainees will be doing in the section.
Remember that many people reading your materials will likely be novices,
so make sure to explain all the relevant concepts.

## Title for a subsection
Section and subsection titles will be displayed in the tutorial index on the left side of
the page, so try to make them informative and concise!
## Bioimage data

# Hands-on Sections
Below are a series of hand-on boxes, one for each tool in your workflow file.
Often you may wish to combine several boxes into one or make other adjustments such
as breaking the tutorial into sections, we encourage you to make such changes as you
see fit, this is just a starting point :)
This tutorial will use an image dataset from the [BioImage archive](https://www.ebi.ac.uk/bioimage-archive/). This dataset is specifically prepared for training nuclear segmentation.

Anywhere you find the word "***TODO***", there is something that needs to be changed
depending on the specifics of your tutorial.
The images are saved in the BioImage archive and can be uploaded to the Galaxy server with the corresponding BioImage Archive retrieval tool.

have fun!
![S-BIAD634:IM276 dataset](../../images/voronoi-segmentation/BIAD634_IM276.png "An annotated fluorescence image dataset for training nuclear segmentation methods")

## Get data
> <hands-on-title>Data upload with Bioimage Archive Tool</hands-on-title>
>
> 1. Create a new history for this tutorial.
> When you log in for the first time, an empty, unnamed history is created by default. You can simply rename it.
>
> {% snippet faqs/galaxy/histories_create_new.md %}
>
> 2. {% tool [FTP Link for BioImage Archive](toolshed.g2.bx.psu.edu/repos/bgruening/bia_download/bia_download/0.1.0+galaxy0) %} with the following parameters:
> - {% icon param-file %} *"Storage mode"*: `fire` (Storage mode is always fire)
> - *"The path of accession"*: `S-BIAD/634/S-BIAD634`
> > <comment-title> BioImage Archive </comment-title>
> >
> > This tool will upload all the files into your Galaxy history which can be very inconvenient when you have large dataset.
> > In that case, you can delete data files you do not plan to use for your analysis.
> {: .comment}
>
> 3. Rename {% icon galaxy-pencil %} the file `Neuroblastoma_0.tif` to `input_image.tif`
> 4. Check that the datatype
>
> {% snippet faqs/galaxy/datasets_change_datatype.md datatype="datatypes" %}
>
> 5. Add to each database a tag corresponding to `input`
>
> {% snippet faqs/galaxy/datasets_add_tag.md %}
>
>
{: .hands_on}

## Earth Observation (EO) data

> <hands-on-title> Data Upload </hands-on-title>
![Datasets of SH's AI4ER MRes Project](https://edsbook.org/_images/7d3b3ce159046d8da12d413a00c69137e4a073dcf1ee27d7cd4e33af6d93d526.png "a top-down RGB image of forest, captured by drone, aircraft or satellite.")

> <hands-on-title> EO Data Upload </hands-on-title>
>
> 1. Create a new history for this tutorial.
> When you log in for the first time, an empty, unnamed history is created by default. You can simply rename it.
>
> {% snippet faqs/galaxy/histories_create_new.md %}
>
> 1. Create a new history for this tutorial
> 2. Import the files from [Zenodo]({{ page.zenodo_link }}) or from
> the shared data library (`GTN - Material` -> `{{ page.topic_name }}`
> -> `{{ page.title }}`):
>
> - **Important:** If setting the type to 'Auto-detect', make sure that after upload, the datatype is set to tiff.
>
> ```
>
> https://zenodo.org/records/5494629/files/Sep_2014_RGB_602500_646500.tif
> ```
> ***TODO***: *Add the files by the ones on Zenodo here (if not added)*
>
> ***TODO***: *Remove the useless files (if added)*
>
> {% snippet faqs/galaxy/datasets_import_via_link.md %}
>
> {% snippet faqs/galaxy/datasets_import_from_data_library.md %}
>
> 3. Rename the datasets
> 3. Rename {% icon galaxy-pencil %} the file `Sep_2014_RGB_602500_646500.tif` to `input_image.tif`
> 4. Check that the datatype
>
> {% snippet faqs/galaxy/datasets_change_datatype.md datatype="datatypes" %}
>
> 5. Add to each database a tag corresponding to ...
> 5. Add to each database a tag corresponding to `input`
>
> {% snippet faqs/galaxy/datasets_add_tag.md %}
>
{: .hands_on}
# Title of the section usually corresponding to a big step in the analysis
It comes first a description of the step: some background and some theory.
Some image can be added there to support the theory explanation:
![Alternative text](../../images/image_name "Legend of the image")
The idea is to keep the theory description before quite simple to focus more on the practical part.
***TODO***: *Consider adding a detail box to expand the theory*
> <details-title> More details about the theory </details-title>
>
> But to describe more details, it is possible to use the detail boxes which are expandable
>
{: .details}
A big step can have several subsections or sub steps:
# Data preparation
## Sub-step with **Convert image format**
> <hands-on-title> Task description </hands-on-title>
> <hands-on-title> Select channel for Voronoi Segmentation </hands-on-title>
>
> 1. {% tool [Convert image format](toolshed.g2.bx.psu.edu/repos/imgteam/bfconvert/ip_convertimage/6.7.0+galaxy3) %} with the following parameters:
> - {% icon param-file %} *"Input Image"*: `output` (Input dataset)
> - *"Extract series"*: `All series`
> - *"Extract timepoint"*: `All timepoints`
> - *"Extract channel"*: `Extract channel`
> - *"Channel id"*: `{'id': 2, 'output_name': 'output'}`
> - *"Extract z-slice"*: `All z-slices`
> - *"Extract range"*: `All images`
> - *"Extract crop"*: `Full image`
> - *"Tile image"*: `No tiling`
> - *"Pyramid image"*: `No Pyramid`
>
> ***TODO***: *Check parameter descriptions*
>
> ***TODO***: *Consider adding a comment or tip box*
>
> > <comment-title> short description </comment-title>
> > <comment-title> Why do we need to select a single channel? </comment-title>
> >
> > A comment about the tool or something else. This box can also be in the main text
> > Select a single channel from the input image. Note that some tools number channels starting from 1, while others start from 0.
> {: .comment}
>
{: .hands_on}
***TODO***: *Consider adding a question to test the learners understanding of the previous exercise*
> <question-title></question-title>
>
> 1. Question1?
> 2. Question2?
>
> > <solution-title></solution-title>
> >
> > 1. Answer for question1
> > 2. Answer for question2
> >
> {: .solution}
>
{: .question}
## Sub-step with **Convert image format**
> <hands-on-title> Task description </hands-on-title>
Expand All @@ -182,7 +168,7 @@ A big step can have several subsections or sub steps:
> - *"Extract series"*: `All series`
> - *"Extract timepoint"*: `All timepoints`
> - *"Extract channel"*: `Extract channel`
> - *"Channel id"*: `{'id': 1, 'output_name': 'output'}`
> - *"Channel id"*: `{'id': 2, 'output_name': 'output'}`
> - *"Extract z-slice"*: `All z-slices`
> - *"Extract range"*: `All images`
> - *"Extract crop"*: `Full image`
Expand Down Expand Up @@ -251,40 +237,6 @@ A big step can have several subsections or sub steps:
>
{: .question}
## Sub-step with **Convert single-channel to multi-channel image**
> <hands-on-title> Task description </hands-on-title>
>
> 1. {% tool [Convert single-channel to multi-channel image](toolshed.g2.bx.psu.edu/repos/imgteam/repeat_channels/repeat_channels/1.26.4+galaxy0) %} with the following parameters:
> - {% icon param-file %} *"Input image (single-channel)"*: `output` (output of **Convert image format** {% icon tool %})
>
> ***TODO***: *Check parameter descriptions*
>
> ***TODO***: *Consider adding a comment or tip box*
>
> > <comment-title> short description </comment-title>
> >
> > A comment about the tool or something else. This box can also be in the main text
> {: .comment}
>
{: .hands_on}
***TODO***: *Consider adding a question to test the learners understanding of the previous exercise*
> <question-title></question-title>
>
> 1. Question1?
> 2. Question2?
>
> > <solution-title></solution-title>
> >
> > 1. Answer for question1
> > 2. Answer for question2
> >
> {: .solution}
>
{: .question}
## Sub-step with **Filter 2-D image**
> <hands-on-title> Task description </hands-on-title>
Expand Down Expand Up @@ -361,79 +313,7 @@ A big step can have several subsections or sub steps:
> 1. {% tool [Threshold image](toolshed.g2.bx.psu.edu/repos/imgteam/2d_auto_threshold/ip_threshold/0.18.1+galaxy2) %} with the following parameters:
> - {% icon param-file %} *"Input image"*: `output` (output of **Filter 2-D image** {% icon tool %})
> - *"Thresholding method"*: `Manual`
> - *"Threshold value"*: `{'id': 2, 'output_name': 'output'}`
>
> ***TODO***: *Check parameter descriptions*
>
> ***TODO***: *Consider adding a comment or tip box*
>
> > <comment-title> short description </comment-title>
> >
> > A comment about the tool or something else. This box can also be in the main text
> {: .comment}
>
{: .hands_on}
***TODO***: *Consider adding a question to test the learners understanding of the previous exercise*
> <question-title></question-title>
>
> 1. Question1?
> 2. Question2?
>
> > <solution-title></solution-title>
> >
> > 1. Answer for question1
> > 2. Answer for question2
> >
> {: .solution}
>
{: .question}
## Sub-step with **Count objects in label map**
> <hands-on-title> Task description </hands-on-title>
>
> 1. {% tool [Count objects in label map](toolshed.g2.bx.psu.edu/repos/imgteam/count_objects/ip_count_objects/0.0.5-2) %} with the following parameters:
> - {% icon param-file %} *"Source file"*: `result` (output of **Compute Voronoi tessellation** {% icon tool %})
>
> ***TODO***: *Check parameter descriptions*
>
> ***TODO***: *Consider adding a comment or tip box*
>
> > <comment-title> short description </comment-title>
> >
> > A comment about the tool or something else. This box can also be in the main text
> {: .comment}
>
{: .hands_on}
***TODO***: *Consider adding a question to test the learners understanding of the previous exercise*
> <question-title></question-title>
>
> 1. Question1?
> 2. Question2?
>
> > <solution-title></solution-title>
> >
> > 1. Answer for question1
> > 2. Answer for question2
> >
> {: .solution}
>
{: .question}
## Sub-step with **Extract image features**
> <hands-on-title> Task description </hands-on-title>
>
> 1. {% tool [Extract image features](toolshed.g2.bx.psu.edu/repos/imgteam/2d_feature_extraction/ip_2d_feature_extraction/0.18.1+galaxy0) %} with the following parameters:
> - {% icon param-file %} *"Label map"*: `result` (output of **Compute Voronoi tessellation** {% icon tool %})
> - *"Use the intensity image to compute additional features"*: `Use intensity image`
> - {% icon param-file %} *"Intensity image"*: `output` (output of **Convert image format** {% icon tool %})
> - *"Select features to compute"*: `Select features`
> - *"Available features"*: ``
> - *"Threshold value"*: `{'id': 3, 'output_name': 'output'}`
>
> ***TODO***: *Check parameter descriptions*
>
Expand Down Expand Up @@ -540,42 +420,6 @@ A big step can have several subsections or sub steps:
>
{: .question}
## Sub-step with **Overlay images**
> <hands-on-title> Task description </hands-on-title>
>
> 1. {% tool [Overlay images](toolshed.g2.bx.psu.edu/repos/imgteam/overlay_images/ip_overlay_images/0.0.4+galaxy1) %} with the following parameters:
> - *"Type of the overlay"*: `Linear blending`
> - {% icon param-file %} *"Image #1"*: `output` (output of **Convert single-channel to multi-channel image** {% icon tool %})
> - {% icon param-file %} *"Image #2"*: `output` (output of **Colorize label map** {% icon tool %})
>
> ***TODO***: *Check parameter descriptions*
>
> ***TODO***: *Consider adding a comment or tip box*
>
> > <comment-title> short description </comment-title>
> >
> > A comment about the tool or something else. This box can also be in the main text
> {: .comment}
>
{: .hands_on}
***TODO***: *Consider adding a question to test the learners understanding of the previous exercise*
> <question-title></question-title>
>
> 1. Question1?
> 2. Question2?
>
> > <solution-title></solution-title>
> >
> > 1. Answer for question1
> > 2. Answer for question2
> >
> {: .solution}
>
{: .question}
## Re-arrange
Expand All @@ -588,3 +432,5 @@ Consider merging some hands-on boxes to have a meaningful flow of the analyses*
Sum up the tutorial and the key takeaways here. We encourage adding an overview image of the
pipeline used.

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