Addons - general topic

As you might’ve see, I’ve created two new addons and one script. For know, they doesn’t do much, but, hopefully, you’ll find them useful.

I was also planning to do an addon to prevent FlyWire from recoloring your main cell after each split or merge, but now I think, that might be impossible.
I’m also thinking about a button to remove all points (multicut, path, annotations) with one click. For now, I didn’t start it and not sure, if it would be useful, but it should be doable.
I also wanted to create something like Custom Highlight in Eyewire, but so far without any successes or ideas how to do it. Same with the idea to highlight parents/children of currently selected supervoxel.

You have any ideas for new addons, please let me and others know in this topic. If you have some remarks to the already existing addons, please post them in their topics.

Also, if you’d like to support me or say a “thank you”, you can do it via PayPal. My account name is
But I want to emphasize that there’s absolutely no need to. My scripts are and always will be freely available to all of you.
It’s just in case :slight_smile: Like, sometimes I like to support some creators and like to have an easy way to do it.


I’m not familiar at all with the code you’re working with here, so forgive me for the lay questions.

Is it possible to set/lock a single segment ID to a specific color/hex, so that it remains the same when recolor is used? This wouldn’t address the merge/split issue, but it would help with maintaining orientation if using the random recolor option.

What about a quick click/quick assign segment color? So, perhaps, instead of clicking on the segment hex button and dragging to the preferred color, a single click / shortkey would assign the segment to a preset preferred color? This is another way of dealing with segment recoloring.

In both cases for instance, if my preferred ‘core’ neuron color is light blue, then I can keep the main segment that color either/or through random recolors, or by quick assigning to my preferred color(s).

All good questions :slight_smile:

As for locking a color. It’s already possible, just select the color manually by clicking on the colored rectangle to the right of the segment you want to have fixed. If you select it by hand, it’ll stay until the next split/merge. The other segments will still recolor after pressing the L key.

I was actually thinking about adding a small palette of prefered colors. I prefer mine yellow or lightgreen and it would be nice to quickly reassign them and stick with them until next split/merge.

I will definitely try to do something like that. Thanks for the vote. There are already 2 of us who want such feature, so I guess, I should start working on it soon :smiley:

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i am all for the hotkey on changing colour, perhaps change colour of the segment your cross is on? My problem is that i sometimes need to get a bigger contrast on the colours on two different segments, but it is often difficult to find the segment in the list to change the colour manually when you have a lot of segments, and often when autoasigning they still are very close. Having a palett with the primary/secondary colour to cycle through with a hotkey would solve this.

It would also be very useful to be able to jump to the different segments from the right menu

I was thinking about something like this:

  • a button, which adds an annotation at the place, where the axis currently are (for example, to click right after we get a new cell),
  • a pallete of, let’s say 3-4 colours.
    The annotatied fragment always gets the first color from the palette (even after split or merge - after all, the annotation still should be in the right segment).
    The other 2-3 colours are assigned (randomly) to the next 2-3 fragments from the list.
    If you have more than 3-4 fragments, the rest have colours chosen randomly (as it is now).

I also like the idea of jumping to the correct segments from the menu. I, sometimes, spend much too much time looking for some small pieces, I’ve added earlier.

I will work on both ideas right after I fix some small details with the current addons.


Another thing I’d like to request: “hide all” / “Show all” segments? Checking/unchecking segments always makes me a bit nervous, particular on big bouquets.

Perhaps also a ‘hide all except’ option, so we can hide all segments except our core segment?

You can currently hide all/show all segments by clicking the blue checkbox located at the top of the list of segments (next to the copy all or all visible segments button; see circled box in image). We are missing a “hide all except” option, that I agree would be useful! :slight_smile:



Oh I didn’t realize that! Very useful, thanks - I’ve got a giant bouquet that’s going to need that soon. :grin:

Since we already have “hide all”/“show all” button, I’ll try to add “Hide all except this one” feature. I’ll probably do a Utilities addon, which will have all smaller options, like this one. I’d like to add to in also @annkri’s suggestion to jump to a segment from the right options bar.
But for now, I’m still struggling with the Permanent Colors addon. As for now, Eyewire seems to be much addon-programmer-friendly, than Neuroglancer :smiley: I can’t find a way to programmatically add annotations, to find a segmentId based on coordinates, or to find selected supervoxelId and then find its rootSegmentId. I’ll probably have to relax the addon a little bit and it probably won’t track a segment constantly. Only allow to set colors quickly and survive recoloring, but not splitting/merging. We’ll see.
But first, I have to finish my bouquet cell :smiley:


I’ve updated all the URLs for updating scripts. Before that, you weren’t able to automatically update the scripts, only manual reinstall was helping.
I’ve realized, that I’ve had “Flywire” in the URLs, but “FlyWire” in GitHub repositories, and while the domain part of an URL is case insensitive, the query part is.
Sorry about that.

Here are the correct links, if you’d like to update the addons and made them automatically uprageable in the future (hopefully :smiley: ):


With the new Utilities addon, I’ve almost cleared the requests’ backlog. The only thing left if to try to switch the resolutions bars to a slider. I’m not sure, if I will be able to do it, but if I do, it will probably land in the new addon. Btw. I just found out, that you can scroll with mouse wheel over the bars to change the resolution :D.

If you have any other suggestions or I missed something, let me know.


is it possible to move the different addons in the menu, i am getting both the save and colourpicker on the same area, so not able to use either

Yes. Click the “O” button in the right side of the Dock (O like Organize) and then grab each addon by its title and move it wherever you want (you can even move them outside the Dock.

on the bigger cells i often have trouble with removing segments that belong by accident somewhere other than the area i am working in 3d. Is there possible to have a button that turn of the remove segment with double click when working on cells like that. or even better not able to remove segments added for more than 30 seconds ago while on.

Not sure, if it’s possible, but definitely an idea worth trying. If not possible, maybe I’ll be able to make a history of, lets say, 10 last removed segments.