In the meantime…
v. 0.10
Added a feature, that highlights separated supervoxels after incorrect splitting.
Take a look at the right-hand side of the screen - the points surrounded with the orange border are separated from the rest of the red points.
Didn’t test it thoroughly, so it might not work in some cases, but worked in the couple I’ve done.
that sounds like a useful feature, it take so much time sometimes to find what points are causing the issue sometimes
v. 0.10.1
Jumping to segments should work the way, I’ve described in my previous post. What I did was basically apply the old way of jumping and if it didn’t find a point to jump to, then the new way should be applied.
Because testing is and always was my weakness, I’m not sure, if all cases are covered and if everything works as it should, so please, let me know, if you find something wrong.
v. 0.10.2
Another fix for the “open segment in a new tab” functionality. Previously it didn’t take into account hidden segments, so whenever you’ve opened any of your segments in a new tab, all the invisible segments were there too. And when you’ve opened a hidden segment in a new tab, it changed to not be hidden anymore and the all the other hidden cells were still there (still hidden).
v. 0.10.3
Small update.
When you Ctrl + right-click on any “Copy segment ID” button, all visible segments will be opened in a new tab, while the hidden segments will be removed from that new tab.
v. 0.10.4
Added a button to switch background color between white and black.
The button, as all the others, is hideable/showable in the Options dialog.
Fixed an issue causing, that when the Resolution buttons were hidden, they didn’t show back until the next refresh. Now they should show immediately after clicking the right checkbox.
Think there might be something wrong with the button to switch background, when pressing it is flashing on a white border around the 3d without also changing background, sometimes when refreshing the white background is there and sometimes not. Pasting in the code manually always give a white background at once without the delay.
The delay is because after changing the background, there has to be an interaction with the 3D panel (e.g. moving cursor over it). It can be done programmatically and I’ll try to find a way to do it. For now, it was just a quick update in hope to make the pictures easier.
Why doesn’t always work, I’m not sure. I will test it more and try to improve it.
Edit: it should now work correctly in v. 0.10.5
jump to segment
i think something might be messed up with the order of where the jumping point is. have had several cells now where the jumping point is not where i am expecting it to be, namely the point where i would want to merge together two branches later. i would expect the point to then be there because that is the point the segment was manually added, but instead it is somewhere downwind. Maybe the error is that it was two jumping points and it chose the newest point instead of the oldest?
Thanks for the report.
I’m currently trying to fix various bugs in all the scripts, so will also take a look at this one.
might also be something with deselecting the segment and selecting it again to get the latest updates that are making the problem
is there a -feasible/doable- way of showing a small popup or some other way of showing if a segment is completed if -say- the mouse cursor hovers (and stays in place) over a segment for # seconds?
ie: i hover my cursor over a segment for 5s and a popup says “segment completed” or the segment flashes green (w/o me having double clicked on it to check the lightbulb colour?
Or maybe a way for completed segment(s) to be coloured in 2D w/o activating the 3D?
Looking for a way to make 'farms" lighter on browsers.
Interesting ideas, I’ll take a look at possibilities.
Any way you could add in a button to get the neuropils layer on? if possible i would like one layer for all of them and one layer each for only medulla, only lobulla, only lobula plate, that way we could use hotkeys to turn them of and on individually
yep, that should be doable
There’s also that small neuropil called Accessory Medulla. Do you want it too as a separate layer?
It’s that small violet blob (2 blobs) here:
https://ngl.flywire.ai/?json_url=https://globalv1.flywire-daf.com/nglstate/5329001597894656
Ofc, the final version will be semi-transparent.
it might be useful but i don´t know how at the moment, do you have any idea if there are special celltypes in that area? if not needed it could always be manually removed if the space is needed, i am a bit afraid of getting too many tabs.
I’ve read, it has something with the circardian rythm, but didn’t find any info, about cells specific to that area.
I’m thinking about making options for that, to select, what tabs should be displayed when the “Show neuropils” button is clicked, e.g. Optic Lobe, Medulla, Lobula, Lobula Plate, Accessory Medulla. At the start, all the tabs will be shown, but when a user unchecks any of them, only the checked ones will be shown.
v. 0.11
I was going to fix all issues there are, but since the need for the new functionality appeared, I’m releasing this new version with some fixes and the new thing:
Added new button called “Show neuropils”. By default, it’ll add new tabs called: Optic Lobe, Medulla, Lobula, Lobula Plate and Accessory Medulla. You can click the “Options” button and select, which layers should be shown. You can also hide the “Show neuropils” button from there.
Fixed an error in the console, which was displayed, when a multi-cut split was incorrect.
Btw. the functionality, where separated supervoxels are bordered with an orange frame works only if you click the “Split preview” button first. When you try to click the “Perform mulit-cut” button right away, both the segments won’t be framed and all the segments in 2D will be filled, so you won’t be able to find the incorrect segment(s). It happens also without any addons. It’s just how the neuroglancer works. In other words: always click the “Preview” button first, if there’s a chance, that there will be separated supervoxels. Otherwise you won’t be able to tell, which ones those are.
Centered the “Background” button.
After right-clicking on any of the Copy ID buttons, that segment was opened in a new tab with the same state of visibility as it was before clicking. Now the segment will always be visible in the new tab, no matter, if it was hidden or visible in the old tab.
Show Neuropils is great. I had actually just been trying to figure out how to make an easy method of showing them / referencing them the day before.
I have an observation and (possible?) request.
When I have all of the options checked for Show Neuropils, and press the button, it loads five tabs: Optic Lobe, Medulla, Lobula Plate, Lobula, and Accessory Medulla, as expected. However, the Optic Lobe tab itself has all of the requisite segments added in its render, meaning that these neuropils are all displayed twice, creating a double thick layer for each. The gif below shows just Optic Lobe turned on, followed by each layer, so that you can see that each segment is actually appearing twice.
However, if I set the Neuropils option to ONLY the Optic Lobe, it loads no segments, resulting in a tab with no 3D render.
Is this a goof, or should
Ideally what I’m looking for here is a single tab with all the neuropils added in it, ala the first setting, without the additional layers, but I’m not quite sure if the current behavior is intended.
