Merge remote-tracking branch 'origin/main'

Author: tferr

_pages/people/hinerm.md

@@ -14,25 +14,32 @@ linkedin: pub/mark-hiner/63/984/8b2
 orcid: 0000-0001-9404-7579
 ---
 
-Mark was a member of the core [ImageJ2](/software/imagej2) development team at [LOCI](/orgs/loci) from 2011-2016, earning the title of Champion of ImageJ for his tireless enthusiasm and dedication to the community. He is co-founder of the [SCIFIO](/libs/scifio) project, a robust and extensible library for reading and writing scientific image file formats, and accessible foundation for image format processing. He also developed the [ImageJ-MATLAB](/scripting/matlab) project for [ImageJ2](/software/imagej2)/[MATLAB](/scripting/matlab) interoperability. Mark rejoined the ImageJ2 team in 2020.
+Most recently, Mark has been an ImageJ2 team member since 2020. His areas of interest include Large Language Models (LLMs), training and user experience.  You can follow his latest work [on GitHub](https://github.com/hinerm).
 
-## My work at LOCI
+## Current priorities
 
-After working at [LOCI](/orgs/loci) for two years as a Research Assistant, Mark completed a M.S. degree in computer science and decided to stay on as a Research Intern. Until 2016 he worked as the lead developer on [SCIFIO](/libs/scifio). His primary areas of interest within CS are artificial intelligence, robotics and programming languages.
+These areas came from a recent [Exchange of Experiences](https://forum.image.sc/t/bina-exchange-of-experiences-reflections-and-outcomes-from-aug-25-llm-image-analysis-workshop/116372) through [BINA](https://www.bioimagingnorthamerica.org). As of Oct 2025 they are still experimental, or conceptual. Mark will be focusing on materializing them in the coming year.
 
-You can follow his latest work [on GitHub](https://github.com/hinerm).
+-   {% include github org='imagej' repo='pyimagej' label='PyImageJ' %} as a medium for LLM interaction with ImageJ/Fiji
+-   {% include github org='fiji' repo='fiji-learn' label='Fiji Learn' %}: a "workshop in a box" and extensible framework for training new users in the Fiji ecosystem and 
+-   {% include github org='fiji' repo='fiji-llm' label='Fiji LLM' %}: first-party support for 
 
-Earlier work at LOCI includes:
+## History at LOCI
 
--   Implemented write functionality in BFITK plugins
--   Modified {% include github org='uw-loci' repo='jar2lib' label='Jar2Lib' %} to automatically collect its output C++ libraries into a single location, and compress that directory for easy automation.
--   Added a generic utility library to the Jar2Lib project, which includes methods for consistent JVM invocation.
--   Modified {% include github org='uw-loci' repo='cppwrap-maven-plugin' label='cpp-wrap' %} to account for the changes in Jar2Lib's structure
--   Created a Java Native Interface ([JNI](http://java.sun.com/developer/onlineTraining/Programming/JDCBook/jni.html)) implementation of [BFITK](http://www.loci.wisc.edu/bio-formats/itk).
--   Established benchmarking process to compare three BFITK implementations
--   Reworked the build system for the BFITK plugins - removing [Ant](http://ant.apache.org/) dependency in favor of [CMake](http://www.cmake.org/) post-build commands
--   Modified Jar2Lib to accept user-defined files to append to the automatically generated `CMakeLists.txt` build files, allowing for custom options to be defined.
--   Used user-defined appending of make files to remove Ant dependency for building BF-CPP (stand-alone C++ library of Bio-Formats) by creating a Jar2Lib script
--   Cross-platform testing of BFITK with [FARSIGHT](http://www.farsight-toolkit.org/) toolkit.
--   Creation of comprehensive developer and user [guides](http://www.farsight-toolkit.org/wiki/FARSIGHT_Tutorials/Building_Software/Bio-Formats) for using Bio-Formats with the FARSIGHT toolkit.
--   Contributed to the FARSIGHT toolkit functionality (general usability improvements, such as hotkeys, window focus and a pixel probe).
+After working at [LOCI](/orgs/loci) for two years as a Research Assistant, Mark completed a M.S. degree in computer science and decided to stay on first as a Research Intern and then a full Softwarte Developer. Mark was a member of the core [ImageJ2](/software/imagej2) development team at [LOCI](/orgs/loci) and lead developer and co-founder on [SCIFIO](/libs/scifio) from 2011-2016. He also developed the [ImageJ-MATLAB](/scripting/matlab) project for [ImageJ2](/software/imagej2)/[MATLAB](/scripting/matlab) interoperability.
+
+He earned the title of Champion of ImageJ for his tireless enthusiasm and dedication to the community.
+
+His previous project areas also include:
+-   {% include github org='scijava' repo='scijava' label='SciJava Ops' %}
+-   {% include github org='imagej' repo='pyimagej' label='PyImageJ' %}
+-   {% include github org='uw-loci' repo='jar2lib' label='Jar2Lib' %}
+-   {% include github org='uw-loci' repo='cppwrap-maven-plugin' label='cpp-wrap' %}
+-   [BFITK](http://www.loci.wisc.edu/bio-formats/itk)
+-   Documentation and tutorials throughout the wiki and larger ecosystem
+
+## Experience outside of the ImageJ ecosystem
+
+-   Development of automation and validation tools for organ transplant clinicians
+-   Modernization architectural engineering of [Genvisis](https://genvisis.org)
+-   Contract research as a bench biochemist (once upon a time)

_pages/plugins/bonej.md

@@ -10,7 +10,7 @@ extensions: ["mathjax"]
 
 BoneJ is a collection of skeletal biology plug-ins for ImageJ. This documentation is for the current BoneJ version available through the ImageJ [updater](/plugins/updater). Legacy documentation is provided for old versions (1.x) at [bonej.org](https://bonej.org/).
 
-GPU-accelerated extensions that run orders of magnitude (~100×) faster are being rolled out on a pay-for-play basis in the new `bonej-plus` package. Functionality is similar to the CPU version, with the primary current limitation being a maximum data size of 1 Gpx (c. 1024³ pixels) per image. Where a BoneJ+ GPU-accelerated extension exists, it's marked below with **BoneJ+** and you can find it in the *Plugins>BoneJ>Plus* menu. Payment is managed through purchasing a bean token from [bonej.org/shop](https://bonej.org/shop) and entering it into the token box at *Plugins>BoneJ>Plus>Check Token*. Drop us a line at bonej-at-bonej.org for a coupon to get a free token to try out BoneJ+.
+GPU-accelerated extensions that run orders of magnitude (~100×) faster are being rolled out on a pay-for-play basis in the new `bonej-plus` package. Functionality is similar to the CPU version, with the primary current limitation being a maximum data size of 2 Gpx (c. 2048³ pixels) per image. Where a BoneJ+ GPU-accelerated extension exists, it's marked below with **BoneJ+** and you can find it in the *Plugins>BoneJ>Plus* menu. Payment is managed through purchasing a bean token from [bonej.org/shop](https://bonej.org/shop) and entering it into the token box at *Plugins>BoneJ>Plus>Check Token*. Drop us a line at bonej-at-bonej.org for a coupon to get a free token to try out BoneJ+.
 
 If you use BoneJ in your work please [cite it](#citation).
 
@@ -416,7 +416,7 @@ An 8-bit, binary 2D or 3D image. Hyperstacks are not supported.
 
 Reznikov, N et al. (2016), *Inter-trabecular angle: A parameter of trabecular bone architecture in the human proximal femur that reveals underlying topological motifs*, Acta Biomaterialia, 44: 65--72, [<doi:j.actbio.2016.08.040>](https://doi.org/10.1016/j.actbio.2016.08.040).
 
-## Thickness
+## Thickness (BoneJ+)
 
 Menu path {% include bc path="Plugins | BoneJ | Thickness" %}.
 

_pages/plugins/foci-analyzer.md

@@ -40,8 +40,6 @@ The table is saved as a `.tsv` file, which can be easily opened in other program
 
 ## Installation / Requirements
 
-> ***IMPORTANT NOTE***: Currently StarDist does not function with Fiji-Latest, due to a [TensorFlow issue](https://github.com/fiji/fiji/issues/393). For the time being, please use Fiji-Stable: select the 'Stable' distribution next to the large green download button on [https://fiji.sc/](https://fiji.sc/)).
-
 [Activate](https://imagej.net/update-sites/following) the following Fiji update sites (in the menu bar, via Help -> Update...):
 - Foci-Analyzer
 - 3D ImageJ Suite
@@ -52,8 +50,8 @@ The table is saved as a `.tsv` file, which can be easily opened in other program
 - CSBDeep
 - IJPB-plugins
 - StarDist
-- (TensorFlow) Due to a recent Fiji update, StarDist [may require the TensorFlow Update Site](https://forum.image.sc/t/stardist-error-since-update/107729) to function properly.
-- (SCF MPI CBG) Only if you want to use the foci detection method 'AreaMaxima local maxima detection'
+- TensorFlow
+- (SCF MPI CBG) - Only required if you want to use the foci detection method 'AreaMaxima local maxima detection'
 
 Run Foci Analyzer from the Fiji menu: `Plugins -> Foci Analyzer -> Foci Analyzer`.
 `Combine result files` can be used to pool output `.tsv` files into a single file/table.

_pages/plugins/ridge-detection.md

@@ -116,6 +116,8 @@ This is a list of publications where the plugin was used:
 
 {% include citation doi="10.1088/1367-2630/18/5/055001" %}
 
+{% include citation doi="10.26508/lsa.202000880" %}
+
 # How to cite
 
 We think the best way is to cite the formal method and the used implementation:

_pages/plugins/snt/analysis.md

@@ -261,7 +261,7 @@ The analysis can be performed from the [Analysis menu](/plugins/snt/manual#root-
 
 # Growth Analysis
 
-Growth Analysis provides detailed time-lapse analysis of neuronal  patterns and requires traced paths to be matches across time frames, as detailed in. The Analysis is accessed through the [Path Manager](./manual#path-manager)'s [Time-lapse Utilities](./manual#time-lapse-utilities-) menu.
+Growth Analysis provides detailed time-lapse analysis of neuronal  patterns and requires traced paths to be matches across time frames, as detailed in the [Time-lapse analysis](./walkthroughs#time-lapse-analysis) walkthrough. The Analysis is accessed through the [Path Manager](./manual#path-manager)'s [Time-lapse Utilities](./manual#time-lapse-utilities-) menu.
 
 {% capture timelapse-demo%}
 For parameter validation and configuration comparisons, load the _Hippocampal neuron (DIC timelapse)_ demo dataset ({% include bc path='File|Load Demo Dataset...' %})

_pages/plugins/snt/walkthroughs.md

@@ -345,7 +345,7 @@ Once undesired motion has been mitigated:
 
       - **Output** Whether a plot, a table or both should be created
 
-7. For more complete, thorough measurements, use [Grow Analysis](./analysis/growth-analysis): In addition to growth trajectories, this option classifies motion growth phases, including elongation and retraction events, phase transitions, angular velocity changes, and directional steering.
+7. For more complete, thorough measurements, use [Grow Analysis](./analysis#growth-analysis): In addition to growth trajectories, this option classifies motion growth phases, including elongation and retraction events, phase transitions, angular velocity changes, and directional steering.
 
 
 {% include gallery align="fill" content=