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Update README.md
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@pgleeson
pgleeson authored Nov 21, 2023
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Expand Up @@ -15,7 +15,7 @@ More details on the data can be found [here](data/CanonicalPositions/README.md),

![Screenshot_Canonical.png](https://raw.githubusercontent.com/openworm/NeuroPAL/main/NeuroML2/Screenshot_Canonical.png)

<p align="center"><i>The above image shows the canonical positions and colors <a href="https://www.opensourcebrain.org/projects/neuropal/repository/revisions/main/show/NeuroML2?explorer=https%253A%252F%252Fraw.githubusercontent.com%252Fopenworm%252FNeuroPAL%252Fmain%252FNeuroML2%252FNeuroPAL_Canonical.net.nml">visualised on Open Source Brain</a>.</i></p>
<p align="center"><i>The above image shows the canonical positions and colors <a href="https://v1.opensourcebrain.org/projects/neuropal/repository/revisions/main/show/NeuroML2?explorer=https%253A%252F%252Fraw.githubusercontent.com%252Fopenworm%252FNeuroPAL%252Fmain%252FNeuroML2%252FNeuroPAL_Canonical.net.nml">visualised on Open Source Brain</a>.</i></p>


# Head and tail datasets
Expand All @@ -27,12 +27,12 @@ The dataset released with this publication on positions and colors (as used in F

![Screenshot_HM.png](https://raw.githubusercontent.com/openworm/NeuroPAL/main/NeuroML2/Screenshot_HM.png)

<p align="center"><i>The above image shows the data <a href="https://www.opensourcebrain.org/projects/neuropal/repository/revisions/main/show/NeuroML2?explorer=https%253A%252F%252Fraw.githubusercontent.com%252Fopenworm%252FNeuroPAL%252Fmain%252FNeuroML2%252FNeuroPAL_Herm_Male.net.nml">visualised on Open Source Brain</a>, with the data from the male worm shown in front (head to left, tail to right, shifted to be adjacent), and the equivalent hermaphrodite data behind.</i></p>
<p align="center"><i>The above image shows the data <a href="https://v1.opensourcebrain.org/projects/neuropal/repository/revisions/main/show/NeuroML2?explorer=https%253A%252F%252Fraw.githubusercontent.com%252Fopenworm%252FNeuroPAL%252Fmain%252FNeuroML2%252FNeuroPAL_Herm_Male.net.nml">visualised on Open Source Brain</a>, with the data from the male worm shown in front (head to left, tail to right, shifted to be adjacent), and the equivalent hermaphrodite data behind.</i></p>

# Whole body datasets

Updated data has been provided by Michael Skuhersky on the whole body cell positions and colors. Conversion of this data can be seen [here](https://github.com/openworm/NeuroPAL/blob/main/TestWholeWorm.ipynb).

![Screenshot_Whole.png](https://raw.githubusercontent.com/openworm/NeuroPAL/main/NeuroML2/Screenshot_Whole.png)

<p align="center"><i>The above image shows the whole worm data <a href="https://www.opensourcebrain.org/projects/neuropal/repository/revisions/main/show/NeuroML2?explorer=https%253A%252F%252Fraw.githubusercontent.com%252Fopenworm%252FNeuroPAL%252Fmain%252FNeuroML2%252FNeuroPAL_All_straightened.net.nml">visualised on Open Source Brain</a>. Seven worm reconstructions are shown, and the worm body/layout has been straightened/standardized as described <a href="https://www.biorxiv.org/content/10.1101/2021.06.09.447813v1.full">here</a>.</i></p>
<p align="center"><i>The above image shows the whole worm data <a href="https://v1.opensourcebrain.org/projects/neuropal/repository/revisions/main/show/NeuroML2?explorer=https%253A%252F%252Fraw.githubusercontent.com%252Fopenworm%252FNeuroPAL%252Fmain%252FNeuroML2%252FNeuroPAL_All_straightened.net.nml">visualised on Open Source Brain</a>. Seven worm reconstructions are shown, and the worm body/layout has been straightened/standardized as described <a href="https://www.biorxiv.org/content/10.1101/2021.06.09.447813v1.full">here</a>.</i></p>

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