this will be useful, might have thought wrong about the neuropils coverage option, but what i was really looking for was a option to find partners for one or more starting cells (without loading the partners) and if those partners was already identified this could be helpful in figuring out what kind of cell i was looking at.
For instance i have a few C type cells but not sure if they are C2 or C3. If they connect to a identified L1 or L3 cell it is a C3. Ofc in that example i could have found it out in other ways, but probably useful in other cases.
Oh, now I get it.
Yes, that version should also be possible - one query to the Conectivity API, then “synaptic_partners/60” queries to the Cell Identify API.
I’ll work on it next.
Currently I want to find some more M2 cells and label them all, so programming may take a little while.
Of course, I’ll still leave the current version, beause it works for all/visible cells, while checking types of synaptic partners will probably be for single cells.
You can see all the details about the cell and if you use the in the bottom right corner (Further analysis), you get a list of the incoming and outgoing cells. If a cell on any of that list has been identified, in the last column of the list there will be the label(s):
Oh, you’re right. I thought, it’s updated everyday now. Looks like I was wrong.
Anyway, I was still going to do the tool, you said about; just meant the Codex as an intermediate way to find the right data.
Added an option to show synaptic partners’ labels for the first visible segment.
When you select the option from the top menu, there will be only the source segment’s id displayed vertically for a couple of seconds. After that, you should see something, like this:
The list on the left shows the incoming partners, on the right - outgoing.
If a tag is repeated for more, than one cell, it will be shown only once on the list, with a multiplier next to it (eg. (x2)).
If a cell has more than one tag, only the most recent will be displayed. I’ve decided to do it like that, so the image would be more clear and easier to read.
The synaptic partners, that have not been identified yet, won’t show anywhere on the list.
If anyone needs any additional options, just let me know.
Edit:
v 0.6.1
A fix, for showing statuses, when there are more than 60 cells affected (“Show statuses and labels” feature).
Second edit:
v 0.6.1.1
Further fixes for getting the data, when there are more than 60 cells.
Third edit:
v 0.6.2
Yet another fixes for the statuses.
Also, added more buttons to the feature for better selection of the right cells:
Added a possibility to select, which options should be visible (thanks @annkri). To access the visibility menu, Ctrl + left-click on the dropdown menu and you should see something like this:
Sometimes when I use the addon for “Find common partners for visible” It returns a blank:
And sometimes it simply says “Success” but no window pops up. Any tips? If I wait a while and try again it usually works properly.
Yes, there are some bugs in the addon. I’m planning to hunt them down, but I always put it off.
The thing, that happens to you usually happens when you use the feature more than once without refreshing between the uses. Probably some global variable somewhere or some unfinished fetchings return their results.
Sorry for that. I hope, I’ll find some time to fix this and many other things some day.
Hi! This is a minor bug, but I’m seeing that “show only identified” is pulling green lightbulbs while “show only completed” is pulling purple, from the “actions” menu
Isn’t it like it should be? After all, green ones are identified (i.e. have labels) and purples are completed, but not classified.
Of course, I could do it, so the “show only completed” would show both green and purple ones. However, the assumption was, that a user could filter these 2 groups apart.
i think you should leave it as it is. Or if anything show only identified should show all that is identified also the yellow ones that is identified but not completed, like cells that go outside dataset, but are enogh complete that you can identify the type but not mark them as complete.
I believe, when one identifies a cell, even if it wasn’t completed, it automatically changes its status to identified (and completed), so there aren’t any yellow identified cells. At least, I didn’t see any yellow one with a label.
Yeah as annkri posted we have some cells that are identified but not completed. There are a few of those in the right OL where we can identify for example, an L3 cell but can’t find it’s continuation across the lamina tear to fully complete it.
Hmm, ive definitely seen some cells that are green lightbulb without any completion details, i just assumed having an id turns it green with or without a completion If theyre expected to stay yellow in that case, should i report any i see going forward? or can it be both/either?
Hmm that sounds very weird. Yes, please report any of those segments. The lightbulb should only be green if the cell/segment has been declared complete and it has a label.
The one exception that could possibly result in the situation you described is if the segment was previously part of a completed cell. So it got split and somehow the “completion” and “labeled”’ status stayed with the removed merger segment. Typically that happens if the split segment was where the completion coordinate was located – which is why we ask for folks to position the crosshairs in the main backbone since typically that part of a cell doesn’t change
If theyre expected to stay yellow in that case, should i report any i see going forward? or can it be both/either?