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Update README.md
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alexanderbates authored Nov 11, 2024
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Expand Up @@ -41,6 +41,8 @@ The **crantr** package serves as a wrapper over the [fafbseg](https://github.com
3. Relevant helper functions called from the [bancr](https://github.com/flyconnectome/bancr) package.
3. CRANT project specific data wrangling and browsing code.

![crantb_example_neuron](https://github.com/flyconnectome/crantr/blob/main/inst/images/crantb_example_neuron.png?raw=true)

## Installation

You can install the development version of `crantr` from GitHub:
Expand Down Expand Up @@ -125,6 +127,8 @@ Let us look at some antennal lobe projection neurons.

If you are a collaborator on the project and have access to our [seatable](https://cloud.seatable.io/workspace/62919/dtable/CRANTb/?tid=0000&vid=0000), you can do this:

![ant_table](https://github.com/flyconnectome/crantr/blob/main/inst/images/ant_table.png?raw=true)

```
# load library
library(crantr)
Expand Down Expand Up @@ -171,13 +175,17 @@ plot3d(crantb.surf, col = "lightgrey", alpha = 0.1)
plot3d(pn.meshes)
```

![crantb_example_neuron_meshes](https://github.com/flyconnectome/crantr/blob/main/inst/images/crantb_example_neuron_meshes.png?raw=true)

We can also make this plot in 2D, in the popular `ggplot2` framework.

```r
# ggplot
crant_ggneuron(pn.meshes , volume = crantb.surf)
```

![crantb_example_neuron_ggplot](https://github.com/flyconnectome/crantr/blob/main/inst/images/crantb_example_neuron_ggplot.png?raw=true)

Sometimes it is also useful for work with skeletons, for example for NBLASTing neurons. We can swiftly fetch the L2 skeletons of a neuron,
built from its super-voxel locations using the python library [pcg_skel](https://github.com/AllenInstitute/pcg_skel), as so:

Expand All @@ -192,9 +200,9 @@ plot3d(crantb.surf, col = "lightgrey", alpha = 0.1)

# plot neurons
plot3d(pn.skels, lwd = 1)
plot3d(pn.meshes, alpha = 0.1)
```

![crantb_example_neuron_skeletons](https://github.com/flyconnectome/crantr/blob/main/inst/images/crantb_example_neuron_skeletons.png?raw=true)

## Data Acknowledgment

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