view spot_detection_2d.xml @ 3:a9972c993bed draft default tip

"planemo upload for repository commit ae389b10be46633407effcc6856167f6e8bb2122"
author imgteam
date Sat, 09 Apr 2022 12:47:08 +0000
parents 859dd1c11ac0
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<tool id="ip_spot_detection_2d" name="Spot Detection" version="0.0.3" profile="20.05"> 
    <description>in a 2D image (sequence)</description>
        <requirement type="package" version="2.9.0">imageio</requirement>
        <requirement type="package" version="1.20.2">numpy</requirement>
        <requirement type="package" version="1.2.4">pandas</requirement>
        <requirement type="package" version="0.18.1">scikit-image</requirement>
    <command detect_errors="aggressive">
         python '$__tool_directory__/'
        <param name="fn_in" type="data" format="tiff" label="Image sequence (stack)" />
        <param name="frame_1st" type="integer" value="1" label="Starting time point (1 for the first frame of the stack)" />
        <param name="frame_end" type="integer" value="0" label="Ending time point (0 for the last frame of the stack)" />
        <param name="filter" type="select" label="Choose a detection filter">
            <option value="Gauss" selected="True">Gaussian</option>
            <option value="LoG">Laplacian-of-Gaussian, LoG (more accurate when spots have similar sizes)</option>
        <param name="ssig" type="float" value="1.0" min="0.5" max="10" label="Sigma of the Gaussian (for noise suppression)" />
        <param name="thres" type="float" value="10.0" min="0" max="100" label="Percentage of the global maximal as the threshold for candidate spots" />
        <param name="typ_intens" type="select" label="How to measure the intensities">
            <option value="smoothed" selected="True">Smoothed</option>
            <option value="robust">Robust</option>
        <param name="bndy" type="integer" value="10" min="0" max="50" label="Width (in pixel) of image boundaries where spots will be ignored" />
        <data format="tabular" name="fn_out" />
            <param name="fn_in" value="test_img1.tif"/>
            <param name="frame_1st" value="1"/>
            <param name="frame_end" value="0"/>
            <param name="filter" value="Gauss"/>
            <param name="ssig" value="1"/>
            <param name="thres" value="10"/>
            <param name="typ_intens" value="smoothed"/>
            <param name="bndy" value="10"/>
            <output name="fn_out" value="spots_detected.tsv" ftype="tabular" />
    **What it does**

    This tool detects spots and measures the intensities in a 2D image (sequence).
        <citation type="doi">10.1097/j.pain.0000000000002642</citation>