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uhlmanngroup / splinedist

SplineDist: Automated Cell Segmentation with Spline Curves
BSD 3-Clause "New" or "Revised" License
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Example script/notebook available for pre-trained models? #12

Closed ajinkya-kulkarni closed 1 year ago

ajinkya-kulkarni commented 1 year ago

Hello team, thanks for this repo! I was wondering if you have an example script that shows how to run the pre-trained models on example images?

sohmandal commented 1 year ago

Hi @ajinkya-kulkarni, thank you for your interest in SplineDist.

If you want to do just inference with SplineDist on a set of images, you might like to follow the prediction notebook in the repo. First, you need to update the path to your data in the second cell (from section 'Data'). Then in the fourth cell (from section 'Load trained model') of this notebook, please assign the relevant weight directory name (such as bbbc038_8 from our pre-trained models) as the name parameter. Please make sure that you keep the weight directory inside the models sub-directory inside the SplineDist root directory. If you are using SplineDist for the first time after cloning the repo, this sub-directory will not be there. You can either create it on your own or you can initiate a training session using the training notebook, which will create this models sub-directory at its proper place for you.

Hope this is helpful.

sohmandal commented 1 year ago

Closing this issue now because of inactivity. Please feel free to reopen it.