From 7072045882b23e511329e30105604be19a679c18 Mon Sep 17 00:00:00 2001 From: Alexander Bates Date: Mon, 11 Nov 2024 12:14:43 -0500 Subject: [PATCH] Update README.md --- README.md | 10 +++++++++- 1 file changed, 9 insertions(+), 1 deletion(-) diff --git a/README.md b/README.md index df733e8..3d3a0e0 100644 --- a/README.md +++ b/README.md @@ -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: @@ -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) @@ -171,6 +175,8 @@ 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 @@ -178,6 +184,8 @@ We can also make this plot in 2D, in the popular `ggplot2` framework. 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: @@ -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