Package: napari-skimage-regionprops
napari-skimage-regionprops (nsr)Anapariplugin for measuring properties of labeled objects based onscikit-imageUsage: measure region propertiesFrom the menuTools > Measurement > Regionprops (nsr)you can open a dialog where you can choose an intensity image, a corresponding label image and the features you want to measure:If you want to interface with the labels and see which table row corresponds to which labeled object, use the label picker andactivate theshow selectedcheckbox.If you closed a table and want to reopen it, you can use the menuTools > Measurements > Show table (nsr)to reopen it.You just need to select the labels layer the properties are associated with.For visualizing measurements with different grey values, as parametric images, you can double-click table headers.Usage: measure point intensitiesAnalogously, also the intensity and coordinates of point layers can be measured using the menuTools > Measurement > Measure intensity at point coordinates (nsr).Also these measurements can be visualized by double-clicking table headers:Working with time-lapse and tracking dataNote that tables for time-lapse data should include a column named "frame", which indicates which slice intime the given row refers to. If you want to import your own csv files for time-lapse data make sure to include this column.If you have tracking data where each column specifies measurements for a track instead of a label at a specific time point,this column must not be added.In case you have 2D time-lapse data you need to convert it into a suitable shape using the function:Tools > Utilities > Convert 3D stack to 2D time-lapse (time-slicer),which can be found in thenapari time slicer.Last but not least, make sure that in case of time-lapse data the label image has labels that are subsquently labeled per timepoint.E.g. a dataset where label 5 is missing at timepoint 4 may be visualized incorrectly.Usage: multichannel or multi-label dataIf you want to relate objects from one channels to objects from another channel, you can useTools > Measurement tables > Object Features/Properties (scikit-image, nsr).This plugin module allos you to answer questions like:how many objects I have inside other objects?what is the average intensity of the objects inside other objects?For that, you need at least two labeled images in napari. You can relate objects along with their features.If intensity features are also wanted, then you also need to provide two intensity images.Below, there is a small example on how to use it.Also, take a look atthis example notebook.Usage, programmaticallyYou can also control the tables programmatically. See thisexample notebookfor details on regionprops andthis example notebookfor details on measuring intensity at point coordinates. For creating parametric map images, seethis notebook.FeaturesThe user can select categories of features for feature extraction in the user interface. These categories contain measurements from the scikit-imageregionprops list of measurementslibrary:size:areabbox_areaconvex_areaequivalent_diameterintensity:max_intensitymean_intensitymin_intensitystandard_deviation_intensity (extra_propertiesimplementation using numpy)perimeter:perimeterperimeter_croftonshapemajor_axis_lengthminor_axis_lengthorientationsolidityeccentricityextentferet_diameter_maxlocal_centroidroundness as defined for 2D labelsby ImageJcircularity as defined for 2D labelsby ImageJaspect_ratio as defined for 2D labelsby ImageJposition:centroidbboxweighted_centroidmoments:momentsmoments_centralmoments_humoments_normalizedThisnapariplugin was generated withCookiecutterusing with@napari'scookiecutter-napari-plugintemplate.See alsoThere are other napari plugins with similar functionality for extracting features:morphometricsPartSegnapari-simpleitk-image-processingnapari-cupy-image-processingnapari-pyclesperanto-assistantFurthermore, there are plugins for postprocessing extracted measurementsnapari-feature-classifiernapari-clusters-plotternapari-accelerated-pixel-and-object-classificationInstallationYou can installnapari-skimage-regionpropsviapip:pip install napari-skimage-regionpropsOr if you plan to develop it:git clone https://github.com/haesleinhuepf/napari-skimage-regionprops

cd napari-skimage-regionprops

pip install -e .If there is an error message suggesting that git is not installed, runconda install git.ContributingContributions are very welcome. Tests can be run withtox, please ensurethe coverage at least stays the same before you submit a pull request.LicenseDistributed under the terms of theBSD-3license,"napari-skimage-regionprops" is free and open source softwareIssuesIf you encounter any problems, please create a thread onimage.scalong with a detailed description and tag@haesleinhuepf.