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Example data for advanced workflow

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tischi

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issue commentNEUBIAS/training-resources

Example data for advanced workflow

@tischi, and @seadaisy, I uploaded PLK1 example images (xy_8bit__nuclei_PLK1_control, + inhibition). I think they are noisy enough that a simple threshold gives a rough boundary so either one needs raw image filtering or binary operations to clean up.

If @seadaisy wants to acquire some additional data it could be nice. For instance the KiF11 one could also look at the tubulin phenotype (intensity values). In principle one would need a 2D image (quite small 500-600 pixels) with not too many nuclei so that we can easily separate them. One can acquire images at different quality (one rather low but still visible and a good image in both channels). For an LSM for instance by reducing the line-averaging, laser-power, or detector gain. Thanks

Antonio

tischi

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manerotoni

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add images for workflow

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Merge branch 'master' into workflow_2d_noisyimages

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Antonio Politi

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Merge pull request #98 from manerotoni/workflow_2d_noisyimages Workflow 2d noisyimages

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Additional images for connectivity

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Antonio Politi

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Merge pull request #97 from manerotoni/cca_extraimages Additional images for connectivity

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Connected components

Add explanation (with image) about the different connectivities.

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tischi

issue commentNEUBIAS/training-resources

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Done

tischi

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issue commentNEUBIAS/training-resources

Example data for advanced workflow

Hi both, If needed, we have a plate with fixed cells with PLK1 and KIF11 phenotypes (cells have a nuclear marker and labeled tubulin). I could take images in the condition you need for your teaching. All the best Sabine

tischi

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issue commentNEUBIAS/training-resources

Example data for advanced workflow

In principle site does not harm to provide several workflow example images.

Yes, please go ahead and add more!

tischi

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issue commentNEUBIAS/training-resources

Example data for advanced workflow

Sorry I misunderstood the first question. I thought you wanted an additional image for just median filter explanation. For the workflow shape measurement with filters this looks good. I realized that I have also more examples with PLK1 inhibition. I guess I also have to add some noise :-( .
In principlesite does not harm to provide several workflow example images.
The PLK1 difference is in the morphology and can be quite nicely shown with circularity.

tischi

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issue commentNEUBIAS/training-resources

Example data for advanced workflow

It is incredible how much time it takes to find good example data with just the problem that you want ;-) I ended up "manufacturing" two images, by cropping and adding some noise to raw data that we acquired during a course.

The task would be to develop a workflow that automatically measures that the nuclei on the left are bigger than on the right.

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tischi

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issue commentNEUBIAS/training-resources

Example data for advanced workflow

I think for the advanced workflow also something where we need a bit of object filtering, right?

tischi

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Rendering of java code bug

@tobyhodges

The java code rendering assigns funny colors to words within block comments.

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* This is a comment
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Any chance we could teach it not to do this?

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