TITLE: MBF Bioscience: FAIR Segmentation and Annotation
AUTHORS: Maci Heal

[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">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. </div></div>

[STEPS]
?. [Adding Metadata and Accessing SPARC Vocabularies from SciCrunch]
Launch one of the following MBF Bioscience software with SPARC-mode enabled.
?. [Adding Metadata and Accessing SPARC Vocabularies from SciCrunch]
Open a microscopy image via the Open icon, File>Open, or dragging and dropping into the program window.NOTE: MBF Bioscience software supports a variety of image file formats from common microscopy vendors such as JPX/JP2, TIFF, LIF, ND2, IMS, OIF/OIB, almost all CZI, and more.
?. [Adding Metadata and Accessing SPARC Vocabularies from SciCrunch]
The SPARC Vocabulary Services window will appear. The dialog is displayed so that you can specify subject-specific metadata and gain access to the SciCrunch database to retrieve anatomical terminology lists compliant with FAIR data principles to use during annotation.
?. [Adding Metadata and Accessing SPARC Vocabularies from SciCrunch]
Use the dropdown menu to select the Species associated with the image in the Subject Information section. This is required information necessary to click Begin.
?. [Adding Metadata and Accessing SPARC Vocabularies from SciCrunch]
Enter a Subject ID associated with the image.
?. [Adding Metadata and Accessing SPARC Vocabularies from SciCrunch]
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.
?. [Adding Metadata and Accessing SPARC Vocabularies from SciCrunch]
Use the dropdown menu to select the Organ associated with the image. This is required information necessary to click Begin.
?. [Adding Metadata and Accessing SPARC Vocabularies from SciCrunch]
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.
?. [Adding Metadata and Accessing SPARC Vocabularies from SciCrunch]
Finally, use the dropdown menu to choose an organ-specific Parcellation associated with the image. Note that some may be Species Independent.
?. [Adding Metadata and Accessing SPARC Vocabularies from SciCrunch]
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!
?. [Adding Metadata and Accessing SPARC Vocabularies from SciCrunch]
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.
?. [Adding Metadata and Accessing SPARC Vocabularies from SciCrunch]
If your API Key needs to be updated, select the Update API Key button.
?. [Adding Metadata and Accessing SPARC Vocabularies from SciCrunch]
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.
?. [Marking with FAIR terminology]
In the marker toolbar on the left side of the program, right-click on the marker type you would like to use. Select the option to Rename Marker.
?. [Marking with FAIR terminology]
The SPARC Terms for Markers window will appear. Search for and/or select the term you would like to name the marker and click OK. The example below shows the SciCrunch terms associatedwith the rat heart.
You may also add a marker name by using the Custom Name... button. Simply type in the custom marker name and select OK to apply the custom marker name. Select OK once again in the SPARC Terms for Markers window. Note: Custom names will not have persistent, unique identifiers from SciCrunch.
You can see what the current name of the marker is here:
?. [Marking with FAIR terminology]
You may now select the marker from the marker toolbar and click in the 2D window to place the marker on the image.
To show the number of each marker placed, right-click anywhere on the marker toolbar and enable 'Show Marker Summary'. To show the names of each marker, right-click anywhere on the marker toolbar and enable 'Show Marker Names'.
?. [Marking with FAIR terminology]
To rename markers that are already placed, click on the Select objects icon in the Trace ribbon of the software and select one or more markers in the 2D window you would like to classify.
?. [Marking with FAIR terminology]
Right-click with your mouse to open the marker options menu. Select Rename selected marker(s)...
?. [Marking with FAIR terminology]
Search for and/or select the marker name you would like the selected marker(s) to be renamed as. When you've selected the term you would like to associated with the marker(s), clck OK.
You may also add a marker name by using the Custom Name... button. Simply type in the custom marker name and select OK to apply the custom marker name. Select OK once again in the SPARC Terms for Markers window.
?. [Contouring with FAIR terminology]
Select the Contour icon in the Trace ribbon of the software.
?. [Contouring with FAIR terminology]
Select the Contour Selection button to open the Contour Selection window to choose a contour name for tracing OR use the dropdown menu above the Contour Selection button to select a contour name for tracing.
?. [Contouring with FAIR terminology]
To place a contour on the image in the 2D window, simply click in the image to place contour points. When you have completed your contour, right-click and select either Close Contour to finish your closed contour or End Open Contour to finish your open-ended contour.
Change the method of tracing a contour by right-clicking and selecting one of the following options: Simple click tracing, Rubber line tracing, or Continuous tracing. Simple click tracing will only show the last point traced and you will click to place the next point.Rubber line tracing will show the last point traced as well as a rubber line connected to the cursor to indicate where the next point will be placed after clicking.Continuous tracing allows for the cursor to be used as a continuous pen stroke as long as the mouse button is held down.
?. [Contouring with FAIR terminology]
Use the Load in Terms icon to load in a .csv or .txt file of terms you would like to add to the contour name list.
?. [Contouring with FAIR terminology]
Request new terms be added to the term list by clicking on the Request new terms icon. This will lead you to the SciCrunch website.
?. [Contouring with FAIR terminology]
Repeat contouring process for all anatomical annotations in your sample.
?. [Classifying trees with FAIR terminology]
After tracing the trees or loading in a data file containing trees, you will be able to classify the trees by using the Classify function in the Edit Trees panel of the 3D window.
?. [Classifying trees with FAIR terminology]
In the Tree panel of the 3D window, select the Edit icon.
?. [Classifying trees with FAIR terminology]
In Tree Edit mode, select the Classify icon.
?. [Classifying trees with FAIR terminology]
In Classify mode, select the tree segment(s) in the 3D window you would like to classify.
Once entering Classify mode, all the trees will change to the color gray. Unclassified trees will remain gray.
Select a tree segment by simply clicking on a tree in the 3D window. When selected, a tree segment will show three squares: one on each end of the segment and one in the middle. A tree segment is not always the whole tree, as seen below. To select multiple segments, hold down the Ctrl button and click to select the segments.
?. [Classifying trees with FAIR terminology]
Using the Branch Name dropdown menu, select the branch name you would like to classify the selected branches as.
When a tree segment has been classified, it will change to the color associated with the term selected. Unclassified segments of the tree will remain gray.
?. [Classifying trees with FAIR terminology]
Repeat step 15 for all trees or tree segments you wish to classify.
?. [Classifying vessels with FAIR terminology]
After tracing the vessels or loading in a data file containing vessels, you will be able to classify the vessels by using the Classify function in the Edit Vessels panel of the 3D window.
?. [Classifying vessels with FAIR terminology]
In the Vessel panel of the 3D window, select the Edit icon.
?. [Classifying vessels with FAIR terminology]
In Vessel Edit mode, select the Classify icon.
?. [Classifying vessels with FAIR terminology]
In Classify mode, select the vessel(s) in the 3D window you would like to classify.
Once entering Classify mode, all the vessels will change to the color gray. Unclassified vessels will remain gray.
Select a vessel segment by simply clicking on a vessel in the 3D window. When selected, a vessel segment will show three squares: one on each end of the segment and one in the middle. A vessel segment is not always the whole vessel, as seen below.To select multiple segments, hold down the Ctrl button and click to select the segments.
?. [Classifying vessels with FAIR terminology]
Using the Segment Name dropdown menu, select the segment name you would like to classify the selected vessel segments as.
When a vessel segment has been classified, it will change to the color associated with the term selected. Unclassified segments of the vessel will remain gray.
?. [Classifying vessels with FAIR terminology]
Repeat step 17 for all vessels or vessel segments you wish to classify.
?. [Saving your Data as an XML]
To save the data file, select File > Save As and select Data File.
?. [Saving your Data as an XML]
In the save dialog window, save your data file as an XML Document File (*.xml)