Exploring high throughput microscopy data with Shiny, Plotly and Fiji
Resources for teaching/preparing to teach bioimage analysis
A project aiming to utilize parallelization within SciJava
issue commentNEUBIAS/training-resources
Example data for advanced workflow
f @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
Does it has to be a confocal image? If not, I can do it on a wide- field (very low light intensity should work). Sabine
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I'm going to update these tutorials over the next few days to add more info on making projects etc. Let me know if there is anything else major missing
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issue commentNEUBIAS/training-resources
Example data for advanced workflow
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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
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Additional images for connectivity
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Merge pull request #97 from manerotoni/cca_extraimages Additional images for connectivity
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Add explanation (with image) about the different connectivities.
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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
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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.
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