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VH-Lab / vhlab-microscopyimageanalysis-matlab

Matlab app for analysis of high density imaging data like that from Array Tomography
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volume filtering gets stuck #8

Closed berithi closed 6 years ago

berithi commented 6 years ago

This happens only for the vglut1 dataset in YEL22JAN_1_1... Thanks :-) b.

stevevanhooser commented 6 years ago

I found the problem. My autohistogram function fails if the number of bins in the histogram exceeds 10 billion or so. :) There were some large outliers. I now modified the function so that if it would be too large, it trims the very large values off the edges.

This requires an update to vhlab_mltbx_toolbox, there's actually nothing wrong with vhlab_mlapp_ArrayTomography in this regard.

However, the ROIs in this vglut1 dataset don't look good, and i think it is because the thresholding is not done well. There seems to be a lot of background points, unless I am not understanding what the image is very well.

berithi commented 6 years ago

Thanks! Yes- I was struggling with the thresholding (it included all the nuclei) and I was trying to see if I could get around that problem with the volume filtering... b.

On Sat, Jan 20, 2018 at 9:37 PM, Steve Van Hooser notifications@github.com wrote:

I found the problem. My autohistogram function fails if the number of bins in the histogram exceeds 10 billion or so. :) There were some large outliers. I now modified the function so that if it would be too large, it trims the very large values off the edges.

This requires an update to vhlab_mltbx_toolbox, there's actually nothing wrong with vhlab_mlapp_ArrayTomography in this regard.

However, the ROIs in this vglut1 dataset don't look good, and i think it is because the thresholding is not done well. There seems to be a lot of background points, unless I am not understanding what the image is very well.

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