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Christian Tischer tischi Bioimage Analyst at EMBL Heidelberg

hmbotelho/shinyHTM 4

Exploring high throughput microscopy data with Shiny, Plotly and Fiji

NEUBIAS/training-resources 2

Resources for teaching/preparing to teach bioimage analysis

fiji-hpc/scijava-parallel 0

A project aiming to utilize parallelization within SciJava

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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

tischi

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Tutorials / user guide

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

K-Meech

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issue commentNEUBIAS/training-resources

Example data for advanced workflow

image

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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add images for workflow

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Merge branch 'master' into workflow_2d_noisyimages

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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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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

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Connected components

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

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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completed object measurements

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Merge pull request #96 from manerotoni/measure_shapes completed object measurements

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Merge branch 'master' of https://github.com/NEUBIAS/training-resources

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pixel module fixed

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Merge branch 'master' of https://github.com/NEUBIAS/training-resources into create_links

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binarization activities links

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binarization exercise

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links for spatial calibration

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