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Image paths use 'main' not 'master'
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alexanderbates committed Jul 12, 2024
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Showing 1 changed file with 9 additions and 9 deletions.
18 changes: 9 additions & 9 deletions README.md
Original file line number Diff line number Diff line change
Expand Up @@ -220,7 +220,7 @@ plot3d(an1.left.skel, col = "darkgreen", alpha = 1)
plot3d(an1.right.nucleus, col = "black", alpha = 1, add = TRUE)
plot3d(an1.left.nucleus, col = "black", alpha = 1, add = TRUE)
```
![banc_an1](https://raw.githubusercontent.com/flyconnectome/bancr/master/inst/images/banc_an1.png)
![banc_an1](https://raw.githubusercontent.com/flyconnectome/bancr/main/inst/images/banc_an1.png)

We can also make a 2D image of multiple views using `ggplot2`.

Expand All @@ -245,7 +245,7 @@ banc_neuron_comparison_plot(neuron1 = an1.right.mesh.simp,
# Tip: You may need to hit 'zoom' on the RStudio plot pane, to see finer meshes,
# when filename = NULL.
```
![banc_an_comparison_ggplot2](https://raw.githubusercontent.com/flyconnectome/bancr/master/inst/images/banc_an_comparison_ggplot2.png)
![banc_an_comparison_ggplot2](https://raw.githubusercontent.com/flyconnectome/bancr/main/inst/images/banc_an_comparison_ggplot2.png)

### Left-right mirror *BANC* neurons

Expand All @@ -255,7 +255,7 @@ we can 'mirror' neurons in *BANC* even though it is an asymmetric space.
Here we can see the normal (grey) and mirrored mesh (green). At the moment,
this works less well in the VNC than the brain.

![banc_neuropil_mirrored](https://raw.githubusercontent.com/flyconnectome/bancr/master/inst/images/banc_neuropil_mirrored.png)
![banc_neuropil_mirrored](https://raw.githubusercontent.com/flyconnectome/bancr/main/inst/images/banc_neuropil_mirrored.png)

```r
an1.right.skel.m <- banc_mirror(an1.right.skel, method = "tpsreg")
Expand All @@ -279,21 +279,21 @@ plot3d(an1.left.mesh, col = "chartreuse", alpha = 0.5)
plot3d(an1.right.skel.m, col = "darkred", alpha = 1)
plot3d(an1.left.skel.m, col = "darkgreen", alpha = 1)
```
![banc_ans_mirrored](https://raw.githubusercontent.com/flyconnectome/bancr/master/inst/images/banc_ans_mirrored.png)
![banc_ans_mirrored](https://raw.githubusercontent.com/flyconnectome/bancr/main/inst/images/banc_ans_mirrored.png)

We can also change the view to see, for example, the brain more clearly.

```r
banc_front_view()
```
![banc_ans_mirrored_brain](https://raw.githubusercontent.com/flyconnectome/bancr/master/inst/images/banc_ans_mirrored_brain.png)
![banc_ans_mirrored_brain](https://raw.githubusercontent.com/flyconnectome/bancr/main/inst/images/banc_ans_mirrored_brain.png)

Or the ventral nerve cord.

```r
banc_vnc_view()
```
![banc_ans_mirrored_vnc](https://raw.githubusercontent.com/flyconnectome/bancr/master/inst/images/banc_ans_mirrored_vnc.png)
![banc_ans_mirrored_vnc](https://raw.githubusercontent.com/flyconnectome/bancr/main/inst/images/banc_ans_mirrored_vnc.png)

### Co-plot *FAFB-FlyWire* and Hemibrain neurons

Expand Down Expand Up @@ -331,7 +331,7 @@ nopen3d()
plot3d(JRC2018F.surf, col = "lightgrey", alpha = 0.1)
plot3d(an1.mesh.simp.brain.jrc2018f, col = c("turquoise", "navy"), alpha = 0.75, add = TRUE)
```
![an_banc_jrc2018f](https://raw.githubusercontent.com/flyconnectome/bancr/master/inst/images/an_banc_jrc2018f.png)
![an_banc_jrc2018f](https://raw.githubusercontent.com/flyconnectome/bancr/main/inst/images/an_banc_jrc2018f.png)

We can now read a neuron from *FAFB-FlyWire*. I already know the ID of the
comparable *FAFB-FlyWire* neurons to fetch.
Expand Down Expand Up @@ -369,7 +369,7 @@ reference = "JRC2018F")
# Add to plot
plot3d(fw.an1.meshes.jrc2018f, col = c("red","orange"), alpha = 1, add = TRUE)
```
![an_banc_hemibrain](https://raw.githubusercontent.com/flyconnectome/bancr/master/inst/images/an_banc_fafb.png)
![an_banc_hemibrain](https://raw.githubusercontent.com/flyconnectome/bancr/main/inst/images/an_banc_fafb.png)

We can do the same with the *Hemibrain*.

Expand Down Expand Up @@ -398,7 +398,7 @@ hb.an1.mesh.jrc2018f <- xform_brain(hb.an1.mesh/1000, sample = "JRCFIB2018F", re
plot3d(hb.an1.mesh.jrc2018f , col = c("chartreuse"), alpha = 1, add = TRUE)
```

![an_banc_fafb_hemibrain](https://raw.githubusercontent.com/flyconnectome/bancr/master/inst/images/an_banc_fafb_hemibrain.png)
![an_banc_fafb_hemibrain](https://raw.githubusercontent.com/flyconnectome/bancr/main/inst/images/an_banc_fafb_hemibrain.png)

Now we see all related neurons from three data sets in one space. Awesome!

Expand Down

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