Features question on the segmentation tab

[manoaman]

Hi @jbms

I recently realized that the segmentation tab has a feature to filter on the tagged segmentation properties. Is this configurable from segment_properties/info? Do you have an example how to configure these tags and use the filter feature?

Also, when do I use a "pin" button? Do you have an example?

Thank you!! -m

[jbms]

For the segment properties, refer to the documentation here: https://github.com/google/neuroglancer/blob/master/src/neuroglancer/datasource/precomputed/segment_properties.md

For an example, see here:

gs://h01-release/data/20210601/c3/segment_properties/info

The pin button allows you to display the layer side panels for multiple layers at once.

[manoaman]

Thank you @jbms

I think the example info file along with the doc helped me digest the structure of the properties and relationship to the tags. A couple more questions to further understand the GUI, 1) What do the light green line and the white line in the property bars represent? 2) Do you also have a document on how the query field works? i.e) "#interneuron #L2 NSe>=800 <NSi" (What does <NSi mean here?) "#interneuron #L2 NSe>=800 <NSI |NSIe" "|" is used for turning on the sort in the table? 3) What are the macOS equivalent for the keyboard binding of operating on bars? i.g.) alt ---> option ?

Thank you

[jbms]

The white line shows the distribution of values of the given property for the segments that match all constraints (i.e. the ones shown as results) as an empirical CDF (cumulative distribution function). The teal line shows the distribution of values of the given property for the segments that match all constraints, except any min/max constraints for the given property.

There is no documentation currently for the query syntax, but the interactive controls modify the query and provide a way to see what the syntax is.

"<" means sort results by the property in ascending order, ">" means sort in descending order, and "|" means include in the results table but don't sort by it.

If alt does not work on macOS we will have to define an alternative binding I suppose --- currently there is no separate binding for macOS.

[manoaman]

Thank you @jbms and excuse me for asking beyond segmentation tab. And I apologize in advance if I missed any docs from the readme contents.

Annotation tab; 1) How does the the feature on this tab work? I keep seeing at the bottom with the message "The selected layers (...) does not have an active annotation tool." Could this also be the macOS binding with my mouse? https://github.com/google/neuroglancer/issues/242#issuecomment-691357942 2) Is there a feature to crop out and/or download a mesh object by drawing a boundary lines? For example, cropping a mesh object from a whole brain atlas mesh.

Render tab; 1) How do the "Linked to:" and "Colors linked to:" features work? I tried link/unlink to different layers but I cannot observe the effects. What would be the use case for these features? 2) When the "opacity" knob does not change the opacity level on the rendered mesh while "saturation" knob does, what could be the reason opacity changer is not changing on the segmented mesh? (I'm observing one of my mesh segmentation processed to precomputed format from the original nii.gz (float64 datatype) of my data is experiencing this. Could it be failing for data conversion at some point?)

Thanks again for your help!

[manoaman]

To be more accurate on the opacity changer, "Opacity (3d)" works fine. "Opacity (on)" on 2D image panels seem binary on/off on the planes. Tried stepping the slider by 0.001, and 0.002 seems like a point where opacity suddenly gets turned on. It appears to be the same opacity until reaching at 1 (max).

[stuarteberg]

I have a general question about the segment properties feature, so I'll ask it in this thread:

According to the spec, I can add properties of type label (which shows up in the UI) and number (which also shows up in the UI and can be used in queries), and also description and string. What does neuroglancer do with the latter two (string and description)? When I create properties of those types, they don't seem to appear in the segment list pane. Can they be used in queries somehow? Can they be shown as extra columns in the segment list, just as the number properties can?

(I want to make sure I'm exploiting the segment properties feature to its fullest!)

[manoaman]

@stuarteberg If I understand correctly, I think the "description" appears in the "Selection" block which appears at the bottom of the UI when you right click a segmentation with your mouse. I don't think the h01 example has the description though.

@jbms Do you have a user manual (YouTube video?) with a visual guidance on how "Render" and "Seg." tabs and their UI components work? I've figured quite a bet from experimenting and looking at other examples but it does take quite an effort to understand bits and pieces of very nice features.

[jbms]

Re: description properties: as @manoaman said, they currently only show up in the "Selection" details panel. The same holds for string properties. For example, in the hemibrain dataset the description is used to provide the full name for the ROIs:

Example link

It is not yet supported to display string properties as columns in the segment list, though that could be added without too much difficulty.

[jbms]

They also can't be used in queries currently.

[stuarteberg]

@manoaman @jbms Thanks very much for the above responses; both were useful. I somehow missed the notifications when you originally wrote them.