John Bogovic bogovicj
bogovicj
/ shapeDemo.groovy
Created
April 2, 2024 14:12
ImageJ2 script that displays a Diamond or Hypersphere neighborhood for a given radius
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| #@ DatasetService ds | |
| #@ UIService ui | |
| #@ Long radius = 13 | |
| #@ String (choices={"Diamond", "Hypersphere"}, style="listBox") shapeType | |
| /* | |
| * Displays a Diamond or Hypersphere neighborhood for a given radius | |
| */ | |
| if( shapeType.equals("Diamond")) | |
| shp = new DiamondShape(radius); |
bogovicj
/ skimage_affine.ipynb
Created
March 20, 2024 14:06
Apply an affine or scaling transform with scikit-image
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bogovicj
/ CompressionExamples.java
Created
December 8, 2023 18:16
Create example n5 array datasets for a variety of compression methods.
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| package org.janelia.saalfeldlab.n5.generateExamples; | |
| import org.janelia.saalfeldlab.n5.Bzip2Compression; | |
| import org.janelia.saalfeldlab.n5.Compression; | |
| import org.janelia.saalfeldlab.n5.GzipCompression; | |
| import org.janelia.saalfeldlab.n5.Lz4Compression; | |
| import org.janelia.saalfeldlab.n5.N5Writer; | |
| import org.janelia.saalfeldlab.n5.RawCompression; | |
| import org.janelia.saalfeldlab.n5.XzCompression; | |
| import org.janelia.saalfeldlab.n5.blosc.BloscCompression; |
bogovicj
/ image_geometry.ipynb
Last active
July 18, 2024 01:12
Image geometry and indexing in python
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| import com.amazonaws.auth.AWSCredentials; | |
| import com.amazonaws.auth.AWSStaticCredentialsProvider; | |
| import com.amazonaws.auth.AnonymousAWSCredentials; | |
| import com.amazonaws.auth.DefaultAWSCredentialsProviderChain; | |
| import com.amazonaws.client.builder.AwsClientBuilder.EndpointConfiguration; | |
| import com.amazonaws.services.s3.AmazonS3; | |
| import com.amazonaws.services.s3.AmazonS3ClientBuilder; | |
| import com.amazonaws.services.s3.model.ListObjectsV2Request; | |
bogovicj
/ iterateRows.groovy
Created
June 22, 2023 20:57
ImageJ2 script to perform an operation over the rows of a dataset
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| #@ Dataset img | |
| /** | |
| * Perform an operation on every row of the input image. | |
| * | |
| * This sets every pixel in the first row to have value zero, | |
| * the second row will have value one, etc. | |
| * | |
| * https://forum.image.sc/t/best-way-to-iterate-over-columns-rows/82472 | |
| */ |
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bogovicj
/ composeDfields.groovy
Created
December 22, 2022 21:45
ImageJ2 script to compose displacement fields
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| #@ Dataset da | |
| #@ Dataset db | |
| dap = Views.moveAxis( da, 2, 0 ); | |
| dbp = Views.moveAxis( da, 2, 0 ); | |
| spacing = [1, 1, 1] as double[]; | |
| dfA = new DisplacementFieldTransform( dap, spacing ); | |
| dfB = new DisplacementFieldTransform( dbp, spacing ); |
bogovicj
/ WorldCup2022.ipynb
Created
November 20, 2022 17:06
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bogovicj
/ zarrQuantization.ipynb
Created
September 29, 2022 18:29
Quantizing and compressing with zarr.
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