Yes, it would definitely help, if the info, if the cell is already labeled, was visible directly in FW. It would be even more useful, if the label itself was directly visible. It would help finding misidentified cells and fixing them.
2 Likes
@Amy would definitely be very helpful beeing able to see if there is a label in FW, and beeing able to see what that label is directly in FW would be useful.
Beeing able to sort trough completed, unlabeled cells etc would probably be useful, when we get the dataset completed enogh that the primary consern is labeling old cells instead of trasing new ones. The problem i think is that there is 100 different way to label one cell type and we need to have a consistent way to label each cell to make it searchable (the list made by kk help a lot in this) but still not every entry will have the same details like tm instead of tm2 and they would need to be gone trough another time to get the exact label, and having the ai help suggest names would probably help here, but is there any way the ai could go trough every cell in the neuropil and suggest batches without us having to manually open every cell?
Opening batches with say 10-50 cells (not sure how many cells you could have without it beeing too much) and looking for/ removing/ marking any that are different from the main type before naming the whole batch, would be much easier than opening one at a time.
1 Like
Hi Krzysztof, I’m attempting to reproduce this trick about changing the resolution through the “Choose image server” dropdown as you describe here. I was able to do this the other week but now I feel like I’m looking in the wrong place. Would you be able to explain this more in depth or confirm for me that the feature seems to have disappeared?
2 Likes
Hi,
You can change the resolution on any image server. Just go the the right panel (make sure, you’re in the segmentation with graph tab) and in the Rendering tab find “Resolution (slice)” thing. Move over it to select the target resolution (e.g. 5px) and click on that bar.
3 Likes
Huh, interestingly I still don’t feel like this is where this info was located when I modified things last week. I could have sworn there were fields to directly input 5 px and then set something to 19/19. I’ve done what you describe but there’s no fields, just that slider, and it’s set to 5 px 27/27. How did you make it 5 px 19/19?
1 Like
The numbers after the px value don’t matter. It’s just the number of chunks already loaded and number of all chunks to be loaded. E.g. 19/19 means, that the currently visible segments consist of 19 chunks and all that chunks have already been loaded.
I’ve forgot to mention in the previous post, but in the “segmentation_with_graph” tab you can set only the resolution of the cross-sections of the visible segments. To set the resolution of the slices (2D images), you have to switch to the “Image” tab (usually the first one at the top) and change the “Resolution (slice)” in there (Rendering tab on the right side). For example, to 5px (again, the numbers after that are not related to the resolution).
2 Likes
Great, okay. So the fractions in the original post were basically there erroneously? 
Thank you!
2 Likes
Yes. At that time, I didn’t know, what the numbers were, so I thought, they are related to the resolution, because they are at the same place as the res.
1 Like
I think, it would be practical, if the multicut points were automatically deleted after a successful cut. I don’t think, they are useful at all after the cut, because they are attached to the old segment (the one before splitting), so can’t be reused for additional cuts anyway.
4 Likes
Hey, thanks for bringing this up and sorry I missed this notification. I designed a new lightbulb menu that was going into production to both make it easier to add annotations and to display them in FlyWire, but we hit some hiccups with lack of confidence in labels (if we display directly within flywire they need to be accurate and not all of them are, some are long, long story…anyway wasn’t able to add it)
Hopefully in the future we can generate some links/spreadsheets of broad classes that can later be used to drill down specifics, like you mentioned in thread earlier today.
3 Likes
i am unable to open any of the link from here Sign in - Google Accounts
it just open a new tab with no dataset or image server chosen and no 2d or 3d, not helping choosing any of the image servers.
Hi annkri,
Uh oh, yes these do seem to be broken. I’ll report this to the devs. Thank you for reporting!
Update: The red annotated coordinate is improperly scaled to FlyWire which is causing the bug. In the meantime, if you zoom out on 2D, eventually the dataset shows. Then right click around on the dataset and your cell will show in 3D. It will look like this: FlyWire (note the red annoated point is far away from the actual 3D mesh)
Fixed the script to accomotade for the new menu:
// ==UserScript==
// @name Temporary fix for menu duplication
// @namespace http://tampermonkey.net/
// @version 0.2.2
// @description Fix
// @author Krzysztof Kruk
// @match https://ngl.flywire.ai/*
// @grant none
// ==/UserScript==
/* globals viewer */
(function() {
'use strict';
setInterval(() => {
const existing = []
const menus = document.getElementsByClassName('neuroglancer-layer-group-viewer-context-menu')
const layer = viewer.saver.pull().state.layers[1]
const segmentsLength = (layer.segments ? layer.segments.length : 0) + (layer.hiddenSegments ? layer.hiddenSegments.length : 0)
if (menus.length > segmentsLength) {
for (let i = menus.length - 1; i > 0; i--) {
const id = menus[i].getElementsByTagName('a')[0].href.split('input_field=')[1].split('=')[0]
if (existing.includes(id)) {
menus[i].remove()
}
else {
existing.push(id)
}
}
}
}, 10000)
})();
2 Likes
This is probably a task for HQ but have you considered if it would be useful to also add label (cell type) if known on the connected cells, shown in the connectivity app. This might help find out what kind of cell it is based on partners with fewer clicks.
And could probably also help finding errors (type x is usually not connected to type z so have to be a merger or wrongly labeled cell)
3 Likes
Agree, it would be very useful. I’ve also thought about it (that HQ should add it). It might be doable via a script, but only when the lightbulbs problem is fixed. Currently it allows only up to about 60 cells to display their status. Because the fix could change the API, I’ll wait with any scripting until it’s done.
is there any way you could make a option on what too show in the action menu. For instance now i am only selecting on the hidden/visible option and would like to tempory hide the other 4 options to make the menu smaller. when working on other types of cell there might be need to use the other selections and perhaps hide the hidden/visible option
1 Like
I’ll look into it.
1 Like
Every once in a while (I have not been able to pin down any specific times or days), I get errors that Identify/Mark Complete are not available. I get this error both with and without KK’s scripts enabled. Pictured below.
The bizarre thing is that when this happens, I am still able to access all the prod.flywire-daf links and use them to manually submit completion or identification. Just not through ngl itself.
I’ve seen this ‘clear up’ in a couple of hours (and it does not affect KK’s mass identifier) but it can be a hiccup when I am working on multiple cell types at once (or even just when I want to ID one specific cell out of a batch different than the rest).
(Note this is not at all similar to the “nightly” downtime of the flywire-daf system which seems to happen sometime between 1-3am Eastern - then even the manual DAF links will result in errors and will not load.)
1 Like
Hi AzureJay,
Thanks for reporting! I’ll pass this along to the devs. You’re not alone as in lab we also have been experiencing the same downtime with the “lightbulb system” (aka the ability to submit labels/complete cells via that menu). I haven’t noticed a particular pattern either… hopefully, with each fix we get closer to stabilizing the issue. Please feel free to also send us reports about the downtime to flywire@eyewire.org
Best,
M.
1 Like