single quote appended to name of channel column about neuroglancer HOT 8 CLOSED

The extra single quote (to make it a local dimension) is added here:

I didn't anticipate that someone would include the special neuroglancer dimension indicators as part of the OME axis names, but I suppose it would make sense to not append a single quote if the dimension name already ends in ' or ^.

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My goal was to be able to programmatically create a URL that "just worked" (i.e. users could open the URL and see the RGB image without having to do any work to flag the channel axis as a channel axis). If there is another way to do that without changing the neuroglancer code, I'm open to it. Adding the ^ to the channel axis name was what I came up with after googling my problem. Granted, I was in a "fast-and-dirty-prototype" state of mind when doing this, so I might have missed something.

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Why is a ' appended to the name of the channel axis. Shouldn't it be a ^? Base on my reading of this

https://github.com/google/neuroglancer/blob/master/src/neuroglancer/coordinate_transform.ts#L636-L638

it seems like channel dimensions are supposed to end with ^ (though I admit there may be something I am not understanding).

As an operational demonstration of my difficulty, this shader code

#uicontrol invlerp normalized(range=[0, 255], channel=2)
void main() {
  emitGrayscale(normalized());
}

doesn't work if the channel name ends with ', but does work if I manually hack the channel name to end with ^.

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If it ends with ', then it is treated as a "local dimension", meaning the layer tab shows a selector for that dimension, and the shader will only have access to the single selected position. However, you can duplicate the layer (probably with a different shader), select a different position for that dimension in the duplicate, and then blend them together.

If it ends with ^, then it is treated as a "channel dimension", which means the shader can access multiple/all positions along that dimension. Neuroglancer currently does not support channel dimensions that are chunked, i.e. where the chunk size along that dimension is not equal to the total extent of that dimension.

In your example where you are using the invlerp control to select just a single channel, you could accomplish the same thing by making it a local dimension rather than a channel dimension. The only case where a channel dimension is needed is if you need a single shader to access more than one channel.

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It is indeed a bit arbitrary whether Neuroglancer makes OME-zarr "channel" dimensions into local dimensions or channel dimensions by default. I decided to make them local dimensions by default because of the limitation on chunking. Changing the name as you have done is in fact the intended mechanism to make it into a channel dimension if that is desired.

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In trying to be as minimally illustrative as possible, I was too simple in my example. My end goal is to have a single shader access all three channels so that I can display an RGB image (and possibly also adjust their relative intensities). Something like

#uicontrol invlerp normalized_r(range=[0, 255.0], channel=0)
#uicontrol invlerp normalized_g(range=[0, 255.0], channel=1)
#uicontrol invlerp normalized_b(range=[0, 255.0], channel=2)

void main() {
  float r = normalized_r();
  float g = normalized_g();
  float b = normalized_b();
  emitRGB(vec3(r,g,b));
}

Again: this works if the channel dimension is named c^, but not if it is named c', which is what the neuroglancer code seems to produce by default.

I admit that changing the one character in the name of the channel dimension is not that difficult, but I am trying to produce a tool that will "just work" for a non-technical user, and I'd rather not ask them to fix the column name unless I absolutely have to.

Is there a way to get shader RGB shader code to work with the current convention?

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You could also accomplish this by having a separate layer for each channel (using c') and enable additive blending mode.

By "produce a tool", can you clarify what you mean? Is your tool generating a Neuroglancer URL/state for the user, that includes this RGB shader? In that case your tool could just rename the dimension as part of the Neuroglancer state.

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Yes. By "produce a tool" I mean "write a script that creates a URL with all the configs necessary to visualize our data."

I did not realize I could rename the dimension in the JSON config. Thank you. I am now unblocked.

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