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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?
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).
Then I clicked upload and move to the next window, where I see everything shown as in the following Screenshot of the window.
I clicked select but no reaction. I then clicked cell division for the frame with two cells but still no reaction.
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.
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.
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:
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:
Screenshot of the uploaded image info in Fiji:
Screenshot of the window:
Downloaded file:
cells.json
cellTypes.json
channels.json
divisions.json
Cell division:
Screenshot of the uploaded image info in Fiji:
Screenshot of the window:
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.
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