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PluginList.wiki
Xiaoxiao Liu edited this page Apr 10, 2015
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Under Mac or Linux, when you run the respective build.macx or build.linux scripts to build Vaa3D from source code (and assume you have checked out all source code and set up the symbolic links correctly - see explanation on this page), you will have the "released" plugins shown in Table below.
- If you run command line, you can type the command
vaa3d -h
(or a similar way to launch the executable, -- depending on your OS) to print all available modules/plugins.
- If you use Vaa3D GUI, you can go to main menu -> Plug-In -> Plug-in Manager.
- If you run command line, you can type the command
vaa3d -h -x <unique_sub_string_of_the_plugin_dynamic_library_file>
to get the available do_menu and do_func lists for this plugin. Then you can directly invoke particular plugin menu or func by using the command
vaa3d -x <unique_sub_string_of_the_plugin_dynamic_library_file> -m <menu_name>
vaa3d -x <unique_sub_string_of_the_plugin_dynamic_library_file> -f <func_name> -i <input image> -o <output> -p <parameter list> -pf <parameter_file>
- If you use Vaa3D GUI, you can go to main menu -> Plug-In and then select any plugin menu you want to run.
The instructions for compiling plugins and running them on Vaa3D platform can be found here.
| Plugin Name | Description | Developer |
|---|---|---|
| Vaa3D plugin creator | A plugin for creating standardized plugin projects | Hang Xiao |
| atlasguided seganno | Atlas-guided recognition and segmentation of cells | Lei Qu, Hanchuan Peng |
| celegans straighten | C. elegans straighten | Lei Qu, Hanchuan Peng |
| bioimageIO Bioformat | Simple image reading using Bioformats library | Yang Yu, Yinan Wan, Hanchuan Peng |
| 5D stack Converter | 5D stack converter | Yang Yu |
| datatype converter | Datatype Converting plugin | Yang Yu |
| Convert Image to AtlasViewMode | Extracts an image's channels and save each of them as a separate image file, and then generates a linker file to link all of them, so that one can use Vaa3D's AtlasViewer to blend/see the data in a more flexible way | Hanchuan Peng |
| blend multiscanstcks | Blend multiple image stacks with various number of color channels, which share a common color channel (reference). | Yang Yu, Hanchuan Peng |
| edge of maskimg | Label the edge of a mask image (label field image)'s edge using either the original label values or white (255) | Hanchuan Peng |
| Distance Transform | Image filter - distance transform | Fuhui Long, Hanchuan Peng |
| Gaussian Filter | Image filter - Gaussian filter | Yang Yu |
| Greyscale Distance Transform | Image filter - greyscale distance transform | Hang Xiao |
| minMaxfilter | Image filter - min/Max filter | Yang Yu |
| montage image sections | Produces a montage view of all z slices | Jinzhu Yang, Hanchuan Peng |
| recenterimage | Recenter an image | Yang Yu |
| Rotate Image | A demo plugin to rotate image in certain plane | Hanchuan Peng |
| ssd registration | Non-rigid image registration | Lei Qu |
| XYZ Resolution | Check and set image voxel xyz resolution --a plugin to show Vaa3D plugin capability | Hanchuan Peng |
| ROI Editor | Edit Regions of Interests (ROIs) of the image of the current window | Jinzhu Yang |
| Label Image Objects | Image segmentation - label image objects by region growing | Yang Yu |
| lobeseger | segments the two optic lobes (OLs) and the center brain (CB) of 3D confocal images of fluit fly brains. It can also segment just one lobe andthe center brain with suitable parameters. | Hanchuan Peng, Hang Xiao |
| ifusion | Image fusion | Yang Yu |
| istitch | Image Stiching | Yang Yu |
| Map View | Mapview version 0.1 | Jinzhu Yang |
| Simple adaptive thresholding | Image thresholding - Simple adaptive thresholding: for each voxel, compute a threshold which is the average intensity of its neighboring voxels and then subtract the threshold from the current voxel's intensity value. | Jinzhu Yang, Hanchuan Peng |
| Linker File Generator | Generate an ano file for all image/object files (sec, apo, tif, lsm, v3draw) in the given directory | Lei Qu, Hanchuan Peng |
| Simple Movie Maker | Simple Movie maker from 3D Viewer | Lei Qu |
| Enhanced SWC Format Converter | Convert between swc and eswc, check eswc correctness | Yinan Wan |
| Global Neuron Feature | Compute global features for a certain neuron | Yinan Wan |
| Resample SWC | Resample neuron swc subject to a fixed step length | Yinan Wan |
| Sort SWC | Reallocate id for the points in 1 neuron (.swc) or mutiple neurons (.ano). Set a new root and sort the SWC file into a new order, where the newly set root has the id of 1, and the parent's id is less than its child's. | Yinan Wan |
| SWC to Maskimage | Convert a SWC file to a mask image, where the area of the swc tubes will have non-zero values, and other area will have 0s. | Jinzhu Yang |
| Canvas Eraser | Canvas Eraser. An early version of plugin demo to show plugin capability | Hanchuan Peng |
| Change Single Pixel Value | Change the value of a single pixel in the image | Yang Yu |
| Principal Skeleton Detection | Detecting the principal skeleton of an image object | Lei Qu |
| refextract | Reference extraction | Yang Yu |
| 3D viewer data push and display | Push plugin | Hanchuan peng, Zongcai Ruan |
| Plugin Call Each Other | Vaa3D Plugin Interface Demo - an example plugin (ex_matrix) called by another plugin (ex_call) | Zongcai Ruan |
| Mouse Event Monitor | Vaa3D Plugin Interface Demo - a demo plugin to monitor the mouse event | Hang Xiao |
| Multi Image Interface | Vaa3D Plugin Interface Demo - V3DPluginInterface demo | Zongcai Ruan |
| Single Image interface | Vaa3D Plugin Interface Demo - V3DSingleImageInterface demo | Zongcai Ruan |
Neuron Tracing
Converting Big-Image-Data
Build Vaa3D Qt6 version on Windows
Build Vaa3D Qt6 version on Ubuntu 20.04