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Some lists (object, trace, and flag) allow you to set which columns are displayed in the table (List>Set columns...). Simply check the names of the columns you wish to display. The column checklists are also available from the Series Options dialog.
Object
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List
The object list allows you to view and modify the attributes of all objects in the series. Remember that an object refers to all traces in a series with the same name.
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The trace list allows you to view and modify the attributes of traces in a single section.
Columns
Index
The index of the trace on the section (its place in the contour).
Tags
The tags that the trace contains.
Length
The length of the trace.
Area
The area of the trace.
Radius
The radius of the trace (the distance from its centroid to the furthest point from the centroid).
Export All
In addition to the regular export option, there is also an export all traces in series option that allows you to export the trace data for every individual trace in the series as a CSV file. This file will have an extra column "section" that indicates the section number where the trace exists.
Filter
In addition to the regex filter, you can filter traces by group and tag. Using multiple types of filters is exclusive; for example, if both a regex and group filter are used, only traces that fit both criteria will be included.
Group
Opening the group filter option (Filter>Group filter...) allows you to enter one or more group name(s) to filter the list. Remember that a group is an identifier that applies to a full object (and not just the individual traces).
The group filter is inclusive; if multiple groups are entered into the filter, all traces within any of the groups will be included in the list.
Tag
Opening the tag filter option (Filter>Tag filter...) allows you to enter one or more tag name(s) to filter the list. Remember that a tag is an identifier that is applied only to a single trace.
The tag filter is inclusive; if multiple tags are entered into the filter, all traces that contain any of the tags in the filter will be included in the list.
Find
Double-clicking on a trace will locate the trace in the field. Additionally, selecting the trace, right-clicking it, and selecting Find will have the same effect.
Modify Trace
Many options in the right-click menu allow you to edit the attributes of one or more trace(s).
Edit
This allows you to edit the name, color, tags, and fill mode of the selected trace(s).
Hide / Unhide
This allows you to hide or unhide the selected trace(s) from display in the field.
Stamp attributes
The options in the stamp attributes menu should only be used on traces that are stamps.
Edit radius allows you to modify the radius of the selected trace(s). The radius is the distance from the centroid to the farthest point on the trace away from the centroid.
Edit shape allows you to modify the shape of the selected trace(s). The radius of each trace is individually preserved.
Delete
This allows you to delete the trace.
Flag List
The flag list allows you to view and modify the attributes of all the flags in the series.
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Columns
Section
The section containing the flag.
Color
The color of the flag.
Flag
The name of the flag.
Resolved
The resolved status of the flag.
Last Comment
The most recent comment of the flag.
Filter
In addition to the regex filter, you can filter flags by resolved status, color, and comment text. Using multiple types of filters is exclusive; for example, if both a regex and color filter are used, only flags that fit both criteria will be included.
Resolved status
In the Filter menu at the top of the list, you can toggle a Display resolved flags option. This option is off by default, meaning that resolved flags will not be displayed in the list.
Color
The Filter>Color Filter menu allows you to filter the flags by a single color.
You can also set the color filter from a selected flag by right-clicking on it and selecting Use as color filter.
Comment text
The Filter>Comment text option allows you to filter the list by flags with a comment that contains the string of text entered by you.
Modify Flags
You can modify a flag by right-clicking on the selected flag.
View / Edit
This allows you to view and modify the name, color, comments, and resolved status of the flag.
Resolve
This menu allows you to mark one or more flag(s) as resolved or unresolved.
Delete
This allows you to delete one or more flag(s).
Delete flags with this name
This allows you to bulk-delete every flag with the name of the selected flag.
Section List
The section list allows you to view and modify the attributes of sections as well as add, remove, and reorder sections.
Columns
Section
The section number (will also contain "(calgrid)" if the section is marked as being a calibration grid).
Thickness
The thickness of the section in microns.
Locked
The locked status of the section ("Locked" or "Unlocked").
Brightness, Contrast
The brightness and contrast of the section, represented a integers between -100 and 100.
Image Source
The name of the image file for the section.
Filter
There are no filters for the section list.
Add, Remove, and Reorder Sections
Insert
Right-clicking on a selected section in the list and navigating to the Insert submenu will allow you to insert a section above or below the selected section.
Delete
Right-clicking on one or more selected section(s) will allow you to delete them.
Reorder sections
Selecting Modify>Reorder sections from the top of the section list will order all sections so that the sections start at zero and count up by one, with the last section number being one less than the total number of sections.
Locking and Unlocking
Many section operations cannot be performed until a section is unlocked. Right-clicking on one or more selected section(s) allows you to lock or unlock them.
Section Thickness
Section thickness can be set by right-clicking on one or more selected section(s) and selecting Edit thickness.
Image Source
The image source is how the section locates the images to display–it is was is searched for in the image directory.
Modify single section
Right-clicking on a selected section and selecting Edit image source will allow you to change the name of the image source.
Modify all sections
Selecting Modify>Section image sources allows you to modify all section image sources at once. This should be used if you have image file names that all match except for the section number.
For example, if your images are named "Image_000.tif", with the last three characters before the file extension representing the section number, you can bulk-modify the section numbers by entering "Image_#.tif" after selecting Modify>Section image sources.
Modify brightness and contrast
Brightness and contrast can be modified in two ways, both accessible by right-clicking the selected section(s) and navigating to the Brightness/contrast submenu.
Set brightness/contrast
This allows you to set the brightness and contrast of the selected section(s) by entering an integer between -100 and 100 for both.
Match brightness/contrast to section in view
This sets the brightness and contrast of the selected section(s) to the brightness and contrast of the section in your viewing field.
Z-trace list
The z-trace list allows you to view and modify the attributes of all z-traces in the series. Remember that a z-trace refers to a curve defined by points in the 3D space. For creating z-traces, see Creating a Z-trace in the Object List section.
Columns
Name
The name of the z-trace. Note that z-trace names are unique–there cannot be two z-traces of the same name in a series.
Start / End
The first/last section in which the z-trace appears.
Distance
The length of the z-trace.
Groups
The groups to which the z-trace belongs.
Alignment
The alignment used to calculate the distance of the z-trace.
Filters
In addition to the regex filter, the object list can be filtered by z-trace group. Using multiple types of filters is exclusive; for example, if both a regex and group filter are used, only objects that fit both criteria will be included.
Group
Opening the group filter option (Filter>Group filter...) allows you to enter one or more group name(s) to filter the list. Remember that a z-trace group is an identifier that applies to a z-trace.
The group filter is inclusive; if multiple groups are entered into the filter, all z-traces within any of the groups will be included in the list.
Modifying a Z-trace
Edit attributes
Right-clicking on a z-trace and selecting Edit attributes allows you to edit the name and color of a z-trace.
Smooth
Right-clicking on a z-trace and selecting Smooth will allow you to smooth a z-trace, making it less jagged. Upon selecting this, you are prompted for a smoothing factor; a higher factor will result in a smoother z-trace. Additionally, you are asked if you would like to create a new z-trace. Unchecking this option will smooth the selected z-trace in place.
Z-trace Groups
Z-trace groups work identically to object groups.
You can add z-traces to groups by right-clicking on one or more selected z-trace(s) in the list and then selecting Group>Add to group...
You can remove z-traces from groups by right-clicking on one or more selected z-trace(s) in the list and then selecting Group>Remove from group... or Group>Remove from all groups...
3D Scene
These options are accessed by right-clicking on selected z-trace(s) and navigating to the 3D submenu option.
Add to scene / Remove from scene
This allows you to add and remove z-traces from the 3D scene. If no 3D scene exists, adding a z-trace or z-traces to the scene will create a scene centered on the z-trace(s).
Change Object Alignment
This allows you to change the associated alignment of a z-trace.
The associated alignment of a z-trace is the alignment that is used when calculating the distance of the z-trace.
If this option is left blank, the current alignment being used in the field will be used.
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