Nuset Segmentation

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. Use 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

Warning

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

Note

min_score & nms_threshold work in opposing ways

Post-process

Export