TITLE: Neurolucida 360: Importing a 3D Organ Scaffold Model for Fiducial Marking
AUTHORS: Maci Heal

[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">How to import a generic 3D organ scaffold model into Neurolucida 360. </div></div>

[STEPS]
?. [Loading an Image, Adding Metadata, and Accessing Vocabularies ]
Launch Neurolucida 360 with SPARC-mode enabled.
?. [Loading an Image, Adding Metadata, and Accessing Vocabularies ]
Open a microscopy image via the Open icon, File>Open, or dragging and dropping into the program window.
?. [Loading an Image, Adding Metadata, and Accessing Vocabularies ]
The SPARC Welcome Window will appear.
?. [Loading an Image, Adding Metadata, and Accessing Vocabularies ]
Use the dropdown menu to select the Species associated with the image in the Subject Information section.
?. [Loading an Image, Adding Metadata, and Accessing Vocabularies ]
Enter a Subject ID associated with the image.
?. [Loading an Image, Adding Metadata, and Accessing Vocabularies ]
Use the dropdown menus to select Sex and Age of the subject associated with the image, or leave as Blinded to condition. Add a numerical value for Age in the textbox.
?. [Loading an Image, Adding Metadata, and Accessing Vocabularies ]
Use the dropdown menu to select the Organ associated with the image.
?. [Loading an Image, Adding Metadata, and Accessing Vocabularies ]
Use the dropdown to select the Species associated with the image, matching it to what was selected in step 3.1. The window will reload so as to provide accurate information for step 3.6. This is required information necessary to click Begin.
?. [Loading an Image, Adding Metadata, and Accessing Vocabularies ]
Finally, use the dropdown menu to choose an organ-specific Parcellation associated with the image. Note that some may be Species Independent.
?. [Loading an Image, Adding Metadata, and Accessing Vocabularies ]
Click Begin to add the selected metadata to the data file when saved and to open the image loaded.
Adding this metadata to a saved data file will allow for FAIR segmentation to occur!
?. [Loading an Image, Adding Metadata, and Accessing Vocabularies ]
You may enable or disable suppression of the SPARC welcome window for the duration of the session you are using the software for by using the Suppress this dialog this session checkbox, which is enabled by default.
?. [Loading an Image, Adding Metadata, and Accessing Vocabularies ]
If your API Key needs to be updated, select the Update API Key button.
?. [Loading an Image, Adding Metadata, and Accessing Vocabularies ]
You may access and update the SPARC Welcome Window information at any time by selecting the Vocabulary Services icon in the Trace ribbon of SPARC mode-enabled MBF software.
?. [Segment ]
Add contours, makers, and/or trees to your image with SPARC vocabulary terms. Save the data as an XML Document File (*.xml). See below protocol for more about this process.
{"blocks":[{"key":"635g5","text":"Segmenting and annotating microscopy image data with MBF Bioscience software using built-in SciCrunch API for up-to-date anatomical terms curated by the SPARC Anatomy Working Group. ","type":"unstyled","depth":0,"inlineStyleRanges":[],"entityRanges":[],"data":[]}],"entityMap":[]}
Example segmentation of a rat heart.
?. [Add Fiducial Marker(s)]
On the left side of the program, you will see a marker toolbar. Right-click and select Show Marker Summary to show the number of each marker placed on the image and Show Marker Name to show the names of each marker.
?. [Add Fiducial Marker(s)]
Right-click on a marker and select Rename Marker to open the SPARC Terms for Markers window. This is where you will select a term for the marker that coincides with a term in the scaffold.
This will become your fiducial marker, a unique anatomical point.
?. [Add Fiducial Marker(s)]
In the SPARC Terms for Markers window, select the anatomical term for your fiducial point. You can search for a term in the search bar and select your term by clicking OK.
In this example, the apex of the heart has been selected.
?. [Add Fiducial Marker(s)]
Place the fiducial marker in the appropriate location of your image. This can occur either in the 2D window or the 3D window.
?. [Add Fiducial Marker(s)]
In the 2D window, navigate to the proper plane and click to place the appropriate fiducial marker from step 9. In the example below, the diamond marker has been renamed apex of the heart.
?. [Add Fiducial Marker(s)]
In the 3D window, select the appropriate fiducial marker from step 9 in the Marker panel and click on the 3D image to place the marker.
?. [Comparing the Segmentation Data to the Scaffold]
Open the 3D window, if not already open.
?. [Comparing the Segmentation Data to the Scaffold]
Select the Import 3D Model icon in the 3D window icon toolbar.
?. [Add Fiducial Marker(s)]
Repeat steps 8-10 as necessary for each fiducial marker.
?. [Download a Scaffold from the SPARC Portal]
Visit sparc.science and search for or select the organ of interest.
?. [Download a Scaffold from the SPARC Portal]
Find and select the scaffold dataset of interest. The example below shows the generic rat heart scaffold.
?. [Download a Scaffold from the SPARC Portal]
Download the scaffold .vtk file from the derivative folder.
?. [Download a Scaffold from the SPARC Portal]
Select Files.
?. [Download a Scaffold from the SPARC Portal]
Select the Derivative folder.
?. [Download a Scaffold from the SPARC Portal]
Select the three dots to the right of the 'mesh' .vtk file and click Download. The example below shows the scaffold .vtk file for the Rat Heart.
?. [Comparing the Segmentation Data to the Scaffold]
Navigate to and select the .vtk mesh scaffold file downloaded in step 14.
?. [Comparing the Segmentation Data to the Scaffold]
A message will pop up asking if you would like to use the marker names found in the file. Select Yes.
?. [Comparing the Segmentation Data to the Scaffold]
The 3D scaffold will load on the left viewport of the 3D window. You will now be able to move each file separately in 3D to compare the scaffold model to your segmentation data. The example below shows the scaffold and segmentation file for a rat heart, where the apex of the heart is labeled Apex and is orange to match the marker of the same name.
?. [Download a Scaffold from the SPARC Portal]
Download the meshMarker.csv file, if one exists, from the derivative folder. Save both .vtk and .csv files in the same directory.