[addon] Cell Identification Helper

#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:

3 Likes
#30

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

2 Likes
#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:

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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.

#41

okay looks like CapsLook is not working very well, only when turning of not on
how about using < instead

1 Like
#42

Unfortunately, I don’t have a Mac so I wasn’t able to check the CapsLock. It works on Windows in both positions.
I was wondering, why you’d like to use <, because it also requires pressing Shift, even on Mac, but then checked the Norwegian layout and understood why :smiley:
But even the < and > keys have functions assigned already - they move the 2D and 3D by some amount of voxels. I wasn’t able to determine, what are the specific rules here, because the movement depends on how the 3D is rotated.
For now, I’ve set the shortcut to the minus sign (-), which looks to be in your keyboard in the same place as is the slash (/) in qwerty keyboards.

Edit:
In v. 0.2.2 also added blocking the shortcuts in textarea and input elements (e.g. chat or cell identificatfion label fields).

1 Like
#43

Thank you,
It looks to be working now. i really appreciate your work making thinks easier, if you could also import the submit cell identification list and use this to choose a label so the labels are build up in the same way for later search that would be perfect.
could ofc just copy the list down myself if it is to much work

1 Like
#44

I was actually thinking about something like this. Maybe a dropdown list with a few of the most common labels added by default and an ability to add own labels and edit/remove all the labels.

#45

what about a full list in the background you can chose from and 3-4 labels in a dropdown menu? ofc that might be little when working on tm cells and the like but think it should cover most cases

1 Like
#46

That would be a few hundreds of entries. But yeah, I think, I could do it.
I also like to add a FlyBrain ID (e.g. FBbt_00003727 for T1) to each cell. It makes them more unique and unequivocal and easier for searching, so maybe I could add also the IDs there.
Other researches also often add that IDs to their identifications.

2 Likes
#47

I was thinking about the same list as you have on the lightbulb, but ofc if you also want to add the Flybrain ID i guess you would need to have it on a simple list with one entry for each cell type?

just to make sure, when using the cell identification helper the cell is both labeled and completed? or do we need to complete it on the lightbulb?

2 Likes