Nuset Segmentation

Deep learning based segmentation, useful for nuclear localized indicators. ROIs segmented through this module can be imported into the Viewer Work Environment.

Parameters

Projection

Choose a projection which maximizes the visibility of your regions of interest

Pre-process

Parameter

Description

do_preprocess

perform pre-processing

do_sigmoid

perform sigmoid correction

sigmoid_cutoff

cutoff, lower values will increase the exposure

sigmoid_gain

gain, high values can be thought of as increasing contrast

sigmoid_invert

invert the image if necessary. Regions of interesting should be bright, background should be dark

do_equalize

perform adaptive histogram equalization

equalize_lower

Set a lower limit, this helps remove background & increase contrast

equalize_upper

Upper limit for the histogram

equalize_kernel

kernel size, increase if the pre-processed image is grainy. Start with a value ~1/16-1/8 the size of the image

NuSeT

Parameter

Description

watershed

wastershed the image, useful if your cells are tightly packed. Uncheck if cells are large and/or sparse.

min_score

Decreasing this value will cause more regions to be found, i.e. cells tend to split more

nms_threshold

Increasing this value will cause more regions to be found, i.e. cells tend to split more

rescale_ratio

Use smaller values less than 1.0 if you have large bright cells, If you have smaller or dim cells use values higher than 1.0

Note

min_score & nms_threshold work in opposing ways

Note

Segmentation will utilize all threads available on your system (regardless of the value set in your System Configuration). However it only takes a few seconds or a few minutes if segmenting a large 3D stack.

Note

high rescale_ratio values will increase the time required for segmentation. Values around 3.0 take about ~1 minute for 512x512 sized images on ~16 core CPUs.

Post-process

Export

If you export using a Convex Hull masks containing only a few pixels, which may be noise, will be removed.

Note

Segmentation will utilize all threads available on your system (regardless of the value set in your System Configuration). However it only takes a few seconds if exporting a 2D image, and make take ~10 minutes if exporting a large 3D stack.