Spot Detection

Based on Extraction of spots in biological images using multiscale products , Jean-Christophe Olivo-Marin Pattern Recognition 35 . This plugin uses currently some GPL code form Icy. To change the threshold factors using flow variables, you have to change the (2 * (n + 1) - 1)th value of the scaleConfig array. For example if you want to change threshold factor 0, you have to change value (2 * (0 + 1) - 1) = 1 of the scaleConfig, or if you want to change threshold factor 2 you have to change the (2 * (2 + 1) - 1) = 5th value in the scaleConfig array.

Options

avg method

The calculated value is used to generate the auto threshold with the formula (3 * value / 0.67) * threshold factor

configure levels

add or remove wavelet levels to determine the number of used levels

• enable: enable the wavelet levels that should be used in the spot detection (at least one)
• threshold factor: use this for fine tuning. The background auto threshold is multiplied by the factor. See node description, if the values should be changed using flow variables.

select dimensions

select a 2d slice for processing

Views

Table Cell View

Workflows

• 01_Spot_DetectionKNIME Hub
• 01_Spot_Detection modif KNIME Forum
• Convex HullKNIME Hub
• Count_Overlapping_Vesicles_8KNIME Forum

Links

• No links available

Developers