Package: guanine-crystal-analysis
guanine-crystal-analysisA plugin for guanine crystal segmentation and classification in the zebrafish eye. More precisely, it provides a workflow that measures on guanine crystal labels and sorts out overlaying partially segmented crystals during classification.Thisnapariplugin was generated withCookiecutterusing@napari'scookiecutter-napari-plugintemplate.UsageThis plugin is suited for users whowant to derive size-, shape and intensity-based parameters from individual guanine crystalsstruggle with partially segmented or overlapping crystalswant to investigate further the size and shape of these guanine crystalsThis plugin is not suited for users whoare interested in further investigations of intensity of guanine crystalsYou can find the plugin in napari underPlugins→guanine-crystal-analysisImage InputThis plugin can be used on individual 2D slices of z-stacks as the workflow was developed on such input.
Therefore, the quality of the result might differ on differing input, like crops or maximum projections.1. NormalizationYou can normalize the image selectingNormalizationwhere you only need to specify your input image and click on theRunbutton.Normalizing the image helps to adjust the intensity values and needs to be applied here because the object segmenter is only trained on normalized images.2. SegmentationWhen selectingSegmentation, you need to select the normalized image and a minimum pixel count of label images and click on theRunbutton again.This avoids having too small and unhelpful labels and is set by default to 50 pixels.
For the training of the model, anAPOCpixel classifier was used.3. Analyze ImageUnderAnalyze Image, you can extract features from your image and label image by selecting them and clicking on theRunbutton.The extracted features are a combination of the two librariesnapari-skimage-regionpropsandnapari-simpleitk-image-processing. They can be devided into size-, shape-, and intensity-based parameters:sizeshapeintensityareaaspect ratiomaximum intensityperimetermean intensitymajor-axis-lengthminimum intensityminor-axis-lengthmediancircularitysumsolidityvarianceeccentricityroundnessperimeter-on-borderperimeter-on-border-ratioYou can find a glossary with an explanation of these featuresin this blog postSome of the guanine crystals are not correctly segmented because of overlay or interference patterns. This problem is addressed with the help of a classification step demonstrated next4. Classify ObjectsYou can divide the crystal labels into predicted (blue) and discarded (brown) crystal labels usingClassify Objects. There you can choose classifiers trained on intensity-, shape- and/or size-based parameters with the help of the checkboxes.For the training of the model, anAPOCobject classifier was used.
It is recommended to later on not measure the parameters that the classifier was trained on, but other ones.5. Bad Label ExclusionNow, you can get rid of the discarded (brown) labels for further analysis usingBad Label Exclusion. Select the two label images of segmentation and classification result and press theRunbutton again.The result is a label image with only the predicted (blue) labels which are relabeled sequentially. If you want to derive measurements on these predicted labels, you can just useAnalyze Imageagain."Analyze Deluxe"You can also do all the explained steps in one click using theAnalyze Deluxefunction.InstallationYou can installguanine-crystal-analysisviapip:pip install guanine-crystal-analysisTo install latest development version :pip install git+https://github.com/biopo/guanine-crystal-analysis.gitContributingContributions are very welcome. Tests can be run withtox, please ensure
the coverage at least stays the same before you submit a pull request.AcknowledgementsThis project was done in collaboration with theRita Mateus Laboratory. The images shown in the documentation and in the demo jupyter notebooks were acquired there.
This project was supported by the Deutsche Forschungsgemeinschaft under Germany’s Excellence Strategy – EXC2068 - Cluster of Excellence "Physics of Life" of TU Dresden.
This project has been made possible in part by grant number2021-240341 (Napari plugin accelerator grant)from the Chan Zuckerberg Initiative DAF, an advised fund of the Silicon Valley Community Foundation.LicenseDistributed under the terms of theBSD-3license,
"guanine-crystal-analysis" is free and open source softwareIssuesIf you encounter any problems, pleasefile an issuealong with a detailed description.