Go to https://github.com/GReD-Clermont/omero_macro-extensions
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Place the two jars files in your Fiji plugin folder (Fiji/plugins)
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Documentation of available commands on the github repository's page: https://github.com/GReD-Clermont/omero_macro-extensions
Codeblock |
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// @String(label="Username") USERNAME
// @String(label="Password", style='password', persist=false) PASSWORD
// @String(label="Host", value='wss://workshop.openmicroscopy.org/omero-ws') HOST
// @Integer(label="Port", value=443) PORT
// @Integer(label="Dataset ID", value=2331) dataset_id |
Codeblock |
user = "my_username"; #@INPUT String (label = "Please enter password", style = password) pwd run("OMERO Extensions"); connected = Ext.connectToOMERO("omero-cai.hhu.de", 4064, user, pwd); // code goes here // don't forget to disconnect at the end of the macro Ext.disconnect()(HOST, PORT, USERNAME, PASSWORD); setBatchMode(true); if(connected == "true") { images = Ext.list("images", "dataset", dataset_id); image_ids = split(images, ","); for(i=0; i<image_ids.length; i++) { ij_id = Ext.getImage(image_ids[i]); ij_id = parseInt(ij_id); roiManager("reset"); run("8-bit"); run("Auto Threshold", "method=MaxEntropy stack"); run("Analyze Particles...", "size=10-Infinity pixel display clear add stack"); run("Set Measurements...", "area mean standard modal min centroid center perimeter bounding summarize feret's median stack display redirect=None decimal=3"); roiManager("Measure"); nROIs = Ext.saveROIs(image_ids[i], ""); print("Image " + image_ids[i] + ": " + nROIs + " ROI(s) saved."); roiManager("reset"); close("Results"); selectImage(ij_id); close(); } } setBatchMode(false); Ext.disconnect(); print("processing done"); |
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