Please have a look at the Fiji/Jython script batch-processing example that runs stardist on all files of a folder. Load default NMS parameters for the selected built-in model.Įxample of running the plugin, showing the returned label image and ROIs overlaid on the input image (check Show All in the ROI Manager):.Increase the number of tiles (in case of GPU memory limitations/errors, i.e.Specify a user-trained model file or URL.The segmented objects can be returned as a Label Image or in the ROI Manager (or both). If in doubt, load the default NMS parameters of the selected built-in model (see below). Overlap Threshold - higher values allow segmented objects to overlap substantially.Probability/Score Threshold - higher values lead to fewer segmented objects, but will likely avoid false positives.If necessary, one can change/disable the percentile-based input image normalization.Īdjust the NMS (non-maximum suppression) postprocessing parameters: A custom user-trained model ( via the training code) that has been exported as a zip file and can be loaded from a file or URL (see Advanced options below).Versatile (H&E nuclei) that was trained on images from the MoNuSeg 2018 training data and the TCGA archive.Versatile (fluorescent nuclei) and DSB 2018 (from StarDist 2D paper) that were both trained on a subset of the DSB 2018 nuclei segmentation challenge dataset.Select a neural network model from the dropdown list, which can be one of the following: Start the plugin from Plugins > StarDist > StarDist 2D. Suitable test images can for instance be found at the Broad Bioimage Benchmark Collection: Note, that currently only 2D and 2D+time images are supported. Click on Apply changes to install the plugin.(If StarDist is missing, click Update URLs to refresh the list of update sites.) Scroll down the list and tick the checkboxes for update sites CSBDeep and StarDist, then click the Close button.Click on the button Manage update sites.
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