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vanvalenlab / deepcell-label

Cloud-based data annotation tools for biological images
https://label.deepcell.org
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Problem on using DeepCell Label to segment and identify cel division event #536

Open lindawang0122ds opened 1 week ago

lindawang0122ds commented 1 week ago

Describe the bug I would like to use DeepCell Label (https://label.deepcell.org/) to generate training dataset however the web could not allow me to select the cells for segmentation when I uploading my tiff images here. Following screenshots show how the window looks like (no reaction). I also tried to identify cell division event to build the lineage but the web also does not allow me to add daughter cells. I also attached the downloaded files from these two frames here. Could you give me some suggestions on that?

Besides, could DeepCell Label generate training/val/test dataset in CTC format (https://celltrackingchallenge.net/datasets/)? Is it the default format or should I adjust some setting to get the CTC format?

https://label.deepcell.org/project?projectId=TzvAxZUckFaP&download=true https://label.deepcell.org/project?projectId=xdhT7tD6Eygc&download=true

To Reproduce Steps to reproduce the behavior:

  1. I upload the tiff sample image to DeepCell Label and select the dimension order be YXC (I'm not sure if it is correct but each image has three channels and has x, y position information but no z stack information).
  2. Then I clicked upload and move to the next window, where I see everything shown as in the following Screenshot of the window.
  3. I clicked select but no reaction. I then clicked cell division for the frame with two cells but still no reaction.
  4. Then I clicked download to downloading all the files attached below.

Expected behavior I expected to see segmentation masks for both frames and when I click "select" and then click the cells in the sample image there should be reaction but it looks like the system can not perform segmentation here. Also when I click "cell division" I expect to add daughter cell ID but the system also has no reaction at all.

Screenshots Cell segmentation: image Screenshot of the uploaded image info in Fiji: Screenshot of the window: image Downloaded file:
cells.json cellTypes.json channels.json divisions.json

Cell division: Screenshot of the uploaded image info in Fiji: image Screenshot of the window: image Downloaded file: cells.json cellTypes.json channels.json divisions.json

Desktop (please complete the following information):

Additional context Add any other context about the problem here.

rossbar commented 6 days ago

I'm not sure I understand the question, so apologies if what I'm saying doesn't make sense.

IIUC, you're uploading individual tiff frames - I don't see how you can perform tracking segmentation across frames if you're uploading them one at a time. You can do this manually of course, but you'd have to handle the divisions manually given that the essential context (e.g. the ID of the parent) is in a separate "project" (since there's only one frame per project).

I'd recommend looking at one of the example projects for cell tracking. To do so, go to label.deepcell.org and try the "corrected tracking timelapse" from the example dropdown menu. Note how there are multiple time frames in this example, which more clearly demonstrates how you can track cell IDs and actions (e.g. divisions) across time.