From 1917850b12296832aa652a99d95acb09cd254ddc Mon Sep 17 00:00:00 2001
From: Curtis Rueden <ctrueden@wisc.edu>
Date: Wed, 26 Mar 2025 16:01:06 -0500
Subject: [PATCH 1/5] Update scripting-clojure: 0.1.6 -> 1.0.0

Which implicitly updates clojure: 1.8.0 -> 1.12.0,
which addresses CVE-2017-20189.
---
 pom.xml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pom.xml b/pom.xml
index 09e985b..5e8f4cd 100644
--- a/pom.xml
+++ b/pom.xml
@@ -418,7 +418,7 @@
 		<org.scijava.scripting-beanshell.version>${scripting-beanshell.version}</org.scijava.scripting-beanshell.version>
 
 		<!-- Scripting: Clojure - https://github.com/scijava/scripting-clojure -->
-		<scripting-clojure.version>0.1.6</scripting-clojure.version>
+		<scripting-clojure.version>1.0.0</scripting-clojure.version>
 		<org.scijava.scripting-clojure.version>${scripting-clojure.version}</org.scijava.scripting-clojure.version>
 
 		<!-- Scripting: Groovy - https://github.com/scijava/scripting-groovy -->

From fda7549fc5120972332104b2bbd1504a4abdff87 Mon Sep 17 00:00:00 2001
From: Caleb Hulbert <cmhulbert@gmail.com>
Date: Tue, 15 Apr 2025 14:56:07 -0400
Subject: [PATCH 2/5] n5 library version bumps

---
 pom.xml | 12 ++++++------
 1 file changed, 6 insertions(+), 6 deletions(-)

diff --git a/pom.xml b/pom.xml
index 5e8f4cd..5325961 100644
--- a/pom.xml
+++ b/pom.xml
@@ -1121,11 +1121,11 @@
 		<net.imglib2.imglib2-label-multisets.version>${imglib2-label-multisets.version}</net.imglib2.imglib2-label-multisets.version>
 
 		<!-- N5 - https://github.com/saalfeldlab/n5 -->
-		<n5.version>3.3.0</n5.version>
+		<n5.version>3.5.0</n5.version>
 		<org.janelia.saalfeldlab.n5.version>${n5.version}</org.janelia.saalfeldlab.n5.version>
 
 		<!-- N5 AWS S3 - https://github.com/saalfeldlab/n5-aws-s3 -->
-		<n5-aws-s3.version>4.2.1</n5-aws-s3.version>
+		<n5-aws-s3.version>4.3.0</n5-aws-s3.version>
 		<org.janelia.saalfeldlab.n5-aws-s3.version>${n5-aws-s3.version}</org.janelia.saalfeldlab.n5-aws-s3.version>
 
 		<!-- N5 Blosc - https://github.com/saalfeldlab/n5-blosc -->
@@ -1133,7 +1133,7 @@
 		<org.janelia.saalfeldlab.n5-blosc.version>${n5-blosc.version}</org.janelia.saalfeldlab.n5-blosc.version>
 
 		<!-- N5 Google Cloud - https://github.com/saalfeldlab/n5-google-cloud -->
-		<n5-google-cloud.version>4.1.1</n5-google-cloud.version>
+		<n5-google-cloud.version>5.1.0</n5-google-cloud.version>
 		<org.janelia.saalfeldlab.n5-google-cloud.version>${n5-google-cloud.version}</org.janelia.saalfeldlab.n5-google-cloud.version>
 
 		<!-- N5 HDF5 Bindings - https://github.com/saalfeldlab/n5-hdf5 -->
@@ -1141,7 +1141,7 @@
 		<org.janelia.saalfeldlab.n5-hdf5.version>${n5-hdf5.version}</org.janelia.saalfeldlab.n5-hdf5.version>
 
 		<!-- N5 ImageJ Bindings - https://github.com/saalfeldlab/n5-ij -->
-		<n5-ij.version>4.2.5</n5-ij.version>
+		<n5-ij.version>4.3.0</n5-ij.version>
 		<org.janelia.saalfeldlab.n5-ij.version>${n5-ij.version}</org.janelia.saalfeldlab.n5-ij.version>
 
 		<!-- N5 ImgLib2 Bindings - https://github.com/saalfeldlab/n5-imglib2 -->
@@ -1149,7 +1149,7 @@
 		<org.janelia.saalfeldlab.n5-imglib2.version>${n5-imglib2.version}</org.janelia.saalfeldlab.n5-imglib2.version>
 
 		<!-- N5 Universe - https://github.com/saalfeldlab/n5-universe -->
-		<n5-universe.version>1.6.0</n5-universe.version>
+		<n5-universe.version>2.3.0</n5-universe.version>
 		<org.janelia.saalfeldlab.n5-universe.version>${n5-universe.version}</org.janelia.saalfeldlab.n5-universe.version>
 
 		<!-- N5 Viewer for Fiji - https://github.com/saalfeldlab/n5-viewer_fiji -->
@@ -1157,7 +1157,7 @@
 		<org.janelia.saalfeldlab.n5-viewer_fiji.version>${n5-viewer_fiji.version}</org.janelia.saalfeldlab.n5-viewer_fiji.version>
 
 		<!-- N5 Zarr - https://github.com/saalfeldlab/n5-zarr -->
-		<n5-zarr.version>1.3.5</n5-zarr.version>
+		<n5-zarr.version>1.5.1</n5-zarr.version>
 		<org.janelia.saalfeldlab.n5-zarr.version>${n5-zarr.version}</org.janelia.saalfeldlab.n5-zarr.version>
 
 		<!-- N5 ZStandard - https://github.com/JaneliaSciComp/n5-zstandard -->

From 88524031d3515d2d8e241c6174d6bfe3da634f72 Mon Sep 17 00:00:00 2001
From: Caleb Hulbert <cmhulbert@gmail.com>
Date: Tue, 15 Apr 2025 15:08:42 -0400
Subject: [PATCH 3/5] bump n5-ij

---
 pom.xml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pom.xml b/pom.xml
index 5325961..888fe5f 100644
--- a/pom.xml
+++ b/pom.xml
@@ -1141,7 +1141,7 @@
 		<org.janelia.saalfeldlab.n5-hdf5.version>${n5-hdf5.version}</org.janelia.saalfeldlab.n5-hdf5.version>
 
 		<!-- N5 ImageJ Bindings - https://github.com/saalfeldlab/n5-ij -->
-		<n5-ij.version>4.3.0</n5-ij.version>
+		<n5-ij.version>4.4.0</n5-ij.version>
 		<org.janelia.saalfeldlab.n5-ij.version>${n5-ij.version}</org.janelia.saalfeldlab.n5-ij.version>
 
 		<!-- N5 ImgLib2 Bindings - https://github.com/saalfeldlab/n5-imglib2 -->

From 11c98b25c42f34d2e5f947f77bd2cb0e36b465c6 Mon Sep 17 00:00:00 2001
From: Caleb Hulbert <cmhulbert@gmail.com>
Date: Tue, 15 Apr 2025 15:55:12 -0400
Subject: [PATCH 4/5] bump n5-hdf5

---
 pom.xml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pom.xml b/pom.xml
index 888fe5f..65bbe74 100644
--- a/pom.xml
+++ b/pom.xml
@@ -1137,7 +1137,7 @@
 		<org.janelia.saalfeldlab.n5-google-cloud.version>${n5-google-cloud.version}</org.janelia.saalfeldlab.n5-google-cloud.version>
 
 		<!-- N5 HDF5 Bindings - https://github.com/saalfeldlab/n5-hdf5 -->
-		<n5-hdf5.version>2.2.0</n5-hdf5.version>
+		<n5-hdf5.version>2.2.1</n5-hdf5.version>
 		<org.janelia.saalfeldlab.n5-hdf5.version>${n5-hdf5.version}</org.janelia.saalfeldlab.n5-hdf5.version>
 
 		<!-- N5 ImageJ Bindings - https://github.com/saalfeldlab/n5-ij -->

From 3f9d1c907373ef0d075e36427bff40d6d272516b Mon Sep 17 00:00:00 2001
From: Curtis Rueden <ctrueden@wisc.edu>
Date: Wed, 16 Apr 2025 14:58:06 -0500
Subject: [PATCH 5/5] Update BigStitcher and multiview-reconstruction

* BigStitcher: 2.0.1 -> 2.5.0
* multiview-reconstruction: 4.1.1 -> 5.4.1
---
 pom.xml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/pom.xml b/pom.xml
index 65bbe74..4596738 100644
--- a/pom.xml
+++ b/pom.xml
@@ -1190,8 +1190,8 @@
 		<net.haesleinhuepf.clijx-weka_.version>${clijx-weka_.version}</net.haesleinhuepf.clijx-weka_.version>
 
 		<!-- BigStitcher - https://imagej.net/plugins/bigstitcher -->
-		<BigStitcher.version>2.0.1</BigStitcher.version>
-		<multiview-reconstruction.version>4.1.1</multiview-reconstruction.version>
+		<BigStitcher.version>2.5.0</BigStitcher.version>
+		<multiview-reconstruction.version>5.4.1</multiview-reconstruction.version>
 		<multiview-simulation.version>0.2.0</multiview-simulation.version>
 		<net.preibisch.BigStitcher.version>${BigStitcher.version}</net.preibisch.BigStitcher.version>
 		<net.preibisch.multiview-reconstruction.version>${multiview-reconstruction.version}</net.preibisch.multiview-reconstruction.version>