[addon] Cell Identification Helper

#21

Ah sorry I always struggle with getting the permissions right on google forms in particular. I updated it so lmk if you still have trouble accessing.

I also added an area to cite the sources you are pulling your updated info from. Hopefully it works now!

2 Likes
#22

Unfortunately, still restricted (at least for me)
Edit: now it works :slight_smile:

1 Like
#23

@AzureJay I’ve just started grouping the cells by neuropils, but I’ve realized, that I don’t know, how to do it, lol.
I mean, R cells start somewhere in Retina, but go through Lamina and some of them also go into Medulla.
L cells start in the space between Retina and Lamina and go through Medulla.
TmY cells start in the same space, but go through all 3 major neuropils.
T and Y also go through all the main neuropils, but start outside the Lobula Plate. But some of them have their CBs between Medulla and LP.
etc., etc.
So it’s hard to tell, where a cell belongs to. At least, I can’t figure out a sensible system.

#24

In the meantime:

v. 0.1

https://raw.githubusercontent.com/ChrisRaven/Flywire-Cell-Identification-Helper/main/Cell-identification-helper.user.js

As always, all suggestions, reports, etc. are more than welcome.

Enjoy! :slight_smile:

3 Likes
#25

I would think either sort it alphabetical or in the way it is done in the guidelines from fishback since that it the way we are used too seeing it. Maybe it would make sense to sort it by neuropil, but before submitting a identification we really should know what type it is, not just guess based on what neuropil it is in, and then i think it would be easier to chose from a alphabetical list.

2 Likes
#26

Currently it is in alphabetical order (if I didn’t mess anything, lol).

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#27

Honestly the order it’s in currently works for me - you’re right in that sorting by neuropil actually gets tricky.

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#28

KK, this is fantastic!

I think the UIUX looks good and that this will be a hugely beneficial feature. The way you have it set up makes sense.

I’ve asked Sven for feedback about authors, years and dois. It could be useful, but it could also potentially make an already messy table even more challenging to clean up.

Let me know if there is anything I can do to help.

3 Likes
#29

Thanks for checking up on it with Sven.
I think, we could add autors, etc. when we find a cell, which isn’t in Fischbach, but in some other well established source.
For now, I’m good, I don’t need anything, but thanks for asking :slight_smile:

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#30

doi in ( ) as you have been doing is good! Sven said just put the most informative name/label first.

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#31

v. 0.1.2

Adds ‘Lamina intrinsic, Lai’ cell
Fixes an error in the console, when completing a cell.

2 Likes
#32

This is so awesome by the way!!

2 Likes
#33

v 0.1.3

Changed Lccn to LLPC and LPLC.

2 Likes
#34

v. 0.2

Added a semi-automatic way to submit labels.

How to use:

  1. You should see a new addition in the Dock:


Click on the “Get cells” button.

  1. There’ll be a dialog window looking like this:

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  1. Enter the label, that you want to add to the cells (e.g. “Lamina wide field 1; Lawf1”) into the “Current label” field and press the “Save” button.

  2. Close the dialog.

  3. Position your cursor in 2D where you would normally position it, if you would like to submit an identification and press the slash (/) key on your keyboard.
    There should be a small green square visible in the top left corner of the screen for a second after a second or two after clicking the key. It indicates, that the point has been successfully saved. If there wasn’t the square, that probably means, that the point doesn’t contain and segments.

  4. Repeat the step 5 for all the cells, that you want to label with the previously set label.

  5. When you’re done with marking the cells, press the “Get cells” button again and you should see a list similar to this one:

1216×871 182 KB

As you can see, you can submit each individual cell, change (edit) its label, remove the entry or jump to the point, you’ve marked for that cell.

At the top there are also two buttosn to do things in batches - either submit all the identifications or remove all the entries.

  1. To submit a cell/all cells, click the appropriate Submit/Submit all button.
    The status of the submitting will be visible in the last column of the table. During submitting the status will say “Submitting…” and be white.
    If the submission was successful the status will change to “Success” in green and the entry will automatically disappear from the table after 1 second.
    If something went wrong, the status will change to a red “Error” and the entry will stay.
    After all statuses had been changed to either “Success” or “Error”, you can resubmit the erroneous ones.

As for marking cells for completion, there are some things, you might find helpful:

  • you don’t have to wait for a cell or a slide to be fully loaded to mark it,
  • you don’t have to have the cell displayed at all. Just be sure, that you’re marking the correct point,
  • you can hide or remove cell immediately after marking it. You don’t even have to wait for the green identificator,
  • you can mark outdated cells. The script looks only on the coords and downloads the most up to date root id associated with them,
  • you can mark several cells one after another without waiting for the green identificator (but you won’t be sure, if all cells have been marked),
  • you don’t have to submit already marked cells before changing the label. So you can mark some cells, change the label, mark others with the new label, etc. and then submit all the changes at once.

I haven’t tested it with really large groups, but submitting about 20 marked cells took maybe 30s and I haven’t have to close any new windows/tabs, so it’s something :slight_smile:

As usual, it’s a new feature, so there might be some bugs. Use with care :wink:

5 Likes
#35

nothing is happening for me clicking on the get cells button

2 Likes
#36

Sorry about that. It was the usual problem with my programming style, lol. I made one thing working, so I’ve moved on, made another thing and so on. Then changed something in the previous things, but because the previous things already did necessary changes in my localStorage/indexedDB, so the latest changes didn’t affect the code on my side. But when somebody makes a fresh start, things break. I should test for such cases, but often I want to publish features as soon as they seem to be working and just forget about the testing.

In the v. 0.2.1 it, hopefully, works ok.

3 Likes
#37

next problem is I don´t have a (/) key on my keyboard, need to use shift + 7 to get it and that is obvious not working. any clue if there are other keys that might be working?

1 Like
#38

oh, I didn’t know, such keyboards exist. I’ve chosen the slash, because it’s close to the right Shift and Ctrl keys, so it makes it easier to fast mark cells.
I can add any other key. Just check what works for you and isn’t already a shortcut for anything in the FW (list of most of the keys is in the Help menu, but there are some keys, that aren’t there, but still do some things).

1 Like
#39

maybe (d) or caps lock might work do not think they are in use?

1 Like
#40

“d” is already used for deleting cells in the Classifier.
Added CapsLock in the v. 0.2.1.1. Now both shortcuts work.