petebankhead
/ QuPath-Threshold pixel classification.groovy
Created
June 14, 2023 08:58
QuPath script to threshold pixel classification outputs with fixed (non-default) threshold values
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| /** | |
| * QuPath v0.4.3 script to threshold probability outputs from a pixel classifier. | |
| * | |
| * By default, converting the pixel classifier output to probabilities will always | |
| * apply a softmax operation and take the class with the highest probability. | |
| * | |
| * This script provides an alternative, whereby you can specify a probability threshold | |
| * for one or more channels, and threshold to create objects from that. | |
| * Using a higher threshold can then restrict the object creation of more confident predictions. | |
| * |
lacan
/ Export Stitched Fields.groovy
Created
October 3, 2024 13:02
[Operetta Importer with Grid/Collection Stitching and Pyramid Export] Using the Operetta Importer with scripting and using the results on the fly to perform stitching #fiji #operetta #groovy #stitching
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| #@ File idFile ( label="'Index.idx.xml' file" ) | |
| #@ File saveFolder ( label="Save Folder", style="directory" ) | |
| // Define stitching parameters. Nothing here is flexible but feel free to try | |
| def params = new mpicbg.stitching.StitchingParameters() | |
| params.channel1 = 0; | |
| params.channel2 = 0; | |
| params.timeSelect = 0; | |
| params.checkPeaks = 5; | |
| params.fusionMethod = 0 |