imagej / imagej.github.io

The ImageJ wiki

ImageJ.net

This repository houses the source of the ImageJ wiki.

Anyone is free to make additions, edits, and improvements; for details, see Editing the Wiki.

Cloning this repository

If you clone this repository, you can use Jekyll to build the site locally. Find instructions in the Advanced Editing guide.

This approach is more complex than editing individual pages via GitHub's online interface, but it is more powerful, with a much faster edit-debug cycle.

Credit

The site theme evolved from Photon by HTML5 UP.

The site makes use of many amazing web libraries and tools, including:

• GitHub Pages + Jekyll + Liquid + kramdown + Rouge
• Typesense + InstantSearch.js + Typesense Instantsearch Adapter
• Citation-js
• Font Awesome
• JS Lightbox + jQuery
• Embed Like Gist
• And all their dependencies! 💖

Our deep gratitude to all the developers and maintainers for this awesome ecosystem of tools—and to all the kind people supporting them with documentation and StackOverflow answers.

imagej.github.io's Issues

make menu buttons "active" on mouseover

pretty minor improvement

Mass convert all existing content

The conversion process involves preprocessing each MediaWiki page, converting it with pandoc, and then postprocessing the result. As of this writing the logic lives in convert/ij_mw_preprocess.py. It is under active development. We need to iteratively convert the codebase, find problems, tweak the conversion script to fix the problems, and repeat until all fixed. 😄 For each iteration, the converted pages should be committed to this repository (at least for now), so that progress is publicly visible as the quality of the converted content improves.

No more MediaWiki-based .md files

This means:

• All Templates and Widgets either converted to includes, inlined or deleted if no longer applicable.
• All pages autoconverted to Markdown, or deleted if no longer applicable.

Bring back menus

The side menus were handled by templates and we need them back, they are currently printed as e.g. %Replace% AboutMenu %Replace% and their content needs to be restored from the wikimedia templates.

Add user table for Fijiyama plugin #40

Hello,
I submitted a pull request on November. It is about updating my plugin page. As I need to make a new page for a new plugin, I would like to know if anything go wrong, or if I can make something else to help.

Nice week to you all !

Converting pages where name includes parentheses

Currently the conversion fails with pages like ImgLib1_(deprecated).mw:

running pandoc on file: ImgLib1_(deprecated).mw
sh: 1: Syntax error: "(" unexpected
Traceback (most recent call last):
  File "mass_convert.py", line 56, in <module>
    iteratively_convert(root_in, root_out, page_title)
  File "mass_convert.py", line 27, in iteratively_convert
    convertLinks(path_out, root_in, root_out)
  File "mass_convert.py", line 48, in convertLinks
    iteratively_convert(root_in, root_out, link)
  File "mass_convert.py", line 27, in iteratively_convert
    convertLinks(path_out, root_in, root_out)
  File "mass_convert.py", line 48, in convertLinks
    iteratively_convert(root_in, root_out, link)
  File "mass_convert.py", line 27, in iteratively_convert
    convertLinks(path_out, root_in, root_out)
  File "mass_convert.py", line 48, in convertLinks
    iteratively_convert(root_in, root_out, link)
  File "mass_convert.py", line 26, in iteratively_convert
    convertFile(path_in, path_out)
  File "mass_convert.py", line 31, in convertFile
    run_pandoc(path_in, path_out)
  File "/media/data/Development/imagej/imagej/imagej.github.io/convert/ij_mw_preprocess.py", line 143, in run_pandoc
    content_tmp = read_file(path_out)
  File "/media/data/Development/imagej/imagej/imagej.github.io/convert/ij_mw_preprocess.py", line 8, in read_file
    with open(file_path) as f:
FileNotFoundError: [Errno 2] No such file or directory: '/home/random/Development/imagej/imagej/imagej.github.io/pages/ImgLib1_(deprecated).md'

Does pandoc not process these file names?

Add community links to front page

maybe also welcome to wiki, and tools?

Conversion: Galleries

This is a mediawiki gallery which should get special attention during conversion:

<gallery>
File:hackathon-2016-konstanz-hackers.jpg|caption|Hackers!
File:hackathon-2016-konstanz-dinner.jpg|caption|Hackers at dinner
File:hackathon-2016-konstanz-rueden.jpg|caption|{{Person|Rueden}}
File:hackathon-2016-konstanz-harrington.jpg|caption|{{Person|Kharrington}}
File:hackathon-2016-konstanz-domander.jpg|caption|{{Person|Rdom}}
File:hackathon-2016-konstanz-hoerl.jpg|caption|{{Person|hoerldavid}}
File:hackathon-2016-konstanz-dietz-and-rueden.jpg|caption|{{Person|Dietzc}} and {{Person|Rueden}}
File:hackathon-2016-konstanz-harrington-and-gunther.jpg|caption|{{Person|Kharrington}} and {{Person|skalarproduktraum}}
File:hackathon-2016-konstanz-helfrich-and-pietzsch.jpg|caption|{{Person|Stelfrich}} and {{Person|Pietzsch}}
File:2016-hackathon-konstanz-sushi.jpg|caption|KNIME 3.2: sushi edition
File:hackathon-2016-konstanz-amazing-salt.jpg|caption|The gravity-defying salt shaker!
</gallery>

Example file: 2016-07-21_-_KNIME_Image_Processing_hackathon.mw

Improve consistency and conciseness of image includes

The image-left, image-right, image-center, and image-fit includes currently use image- prefix for their parameters. But this is probably unnecessary. It increases the length of inclusion declarations. We should consider:

1. Removing the image- prefixes in favor of plain names; and
2. Naming the parameters the same as the HTML img attribute, e.g. src instead of path; and
3. Adding more case logic to enable things like src without relative path defaulting to media/ prefix, so it doesn't need to be manually specified on every include, since the vast majority of image includes will be for images in the media folder.

Conversion: timelines

Pages like 2016-07-21_-_KNIME_Image_Processing_hackathon.mw include timelines which don't work on the new page.

Example (original code):

<timeline>
Preset = TimeHorizontal_AutoPlaceBars_UnitYear

ImageSize = width:600

Colors =
  id:c01 value:blue
  id:c02 value:red
  id:c03 value:green
  id:c04 value:black
  id:c05 value:magenta
  id:c06 value:teal
  id:c07 value:yelloworange
  id:c08 value:skyblue
  id:c09 value:claret
  id:c10 value:oceanblue
  id:c11 value:purple
  id:c12 value:powderblue
  id:c13 value:coral
  id:c14 value:redorange
  id:c15 value:kelleygreen
  id:c16 value:orange
  id:c17 value:lightpurple
  id:c18 value:tan2
  id:c19 value:gray(0.3)
  id:c20 value:blue
  id:c21 value:red
  id:c22 value:green
  id:c23 value:black
  id:c24 value:magenta
  id:c25 value:teal
  id:gridLine value:gray(0.5)
  id:gridCanvas value:gray(0.8)

BackgroundColors = canvas:gridCanvas

Period = from:5 till:14

ScaleMajor = unit:year increment:1 start:5 grid:white

LineData =
  at:5 color:gridLine layer:back width:0.5
  at:6 color:gridLine layer:back width:0.5
  at:7 color:gridLine layer:back width:0.5
  at:8 color:gridLine layer:back width:0.5
  at:9 color:gridLine layer:back width:0.5
  at:10 color:gridLine layer:back width:0.5
  at:11 color:gridLine layer:back width:0.5
  at:12 color:gridLine layer:back width:0.5
  at:13 color:gridLine layer:back width:0.5
  at:14 color:gridLine layer:back width:0.5

BarData=
  barset:Hackers

PlotData=
  width:15 
  fontsize:M
  textcolor:white
  align:left 
  anchor:from 
  shift:(4,-4) 
  color:black

  barSet:Hackers
  color:c01 from:11 till:14 text:"Tim-Oliver Buchholz (UniKN)"
  color:c02 from:8 till:9 text:"Joshy Cyriac (USB, 4Quant)"
  color:c03 from:7 till:13 text:"Richard Domander (RVC)"
  color:c04 from:7 till:10 text:"Kevin Mader (4Quant, ETHZ)"
  color:c05 from:7 till:10 text:"Simon Schmid (UniKN)"
  color:c06 from:7 till:9 text:"Marcel Wiedenmann (UniKN)"
  color:c07 from:7 till:8 text:"Jan Eglinger (FMI Basel)"
  color:c08 from:5 till:13 text:"Kyle Harrington (HMS)"
  color:c09 from:6 till:12 text:"Curtis Rueden (UW-Madison)"
  color:c10 from:5 till:14 text:"Christian Dietz (UniKN)"
  color:c11 from:5 till:14 text:"Patrick Winter (UniKN)"
  color:c12 from:5 till:14 text:"Tobias Pietzsch (MPI-CBG)"
  color:c13 from:5 till:14 text:"Ulrik Günther (MPI-CBG)"
  color:c14 from:5 till:14 text:"Martin Horn (UniKN)"
  color:c15 from:5 till:14 text:"Andreas Burger (UniKN)"
  color:c16 from:5 till:14 text:"Alexander FIllbrunn (UniKN)"
  color:c17 from:5 till:14 text:"David Hörl (LMU Munich / MDC Berlin)"
  color:c18 from:5 till:13 text:"Jonathan Hale (UniKN)"
  color:c19 from:5 till:12 text:"Nico Hoffmann (TUD)"
  color:c20 from:5 till:9 text:"Stefan Helfrich (UniKN)"
  color:c21 from:5 till:8 text:"Cyril Mongis (Uni-Heidelberg)"

</timeline>

Change master -> main on all pages

All main branches have been renamed

Filenames not compatible with windows file systems

Trying to clone the repo in windows gives the following errors:

Cloning into 'imagej.github.io'...
remote: Enumerating objects: 599, done.
remote: Counting objects: 100% (599/599), done.
remote: Compressing objects: 100% (369/369), done.
remote: Total 115468 (delta 315), reused 312 (delta 228), pack-reused 114869
Receiving objects: 100% (115468/115468), 975.80 MiB | 11.37 MiB/s, done.
Resolving deltas: 100% (74288/74288), done.
error: unable to create file _pages/How_to_cite_Fiji?.md: Invalid argument
error: unable to create file media/Simple Neurite Tracer "Export to SWC" Tutorial-1.png: Invalid argument
error: unable to create file media/Simple Neurite Tracer "Export to SWC" Tutorial-3.png: Invalid argument
error: unable to create file media/Simple_Neurite_Tracer_"Export_to_SWC"_Tutorial-2.png: Invalid argument
Checking out files: 100% (5089/5089), done.
warning: the following paths have collided (e.g. case-sensitive paths
on a case-insensitive filesystem) and only one from the same
colliding group is in the working tree:

  'media/ColocByCorrelate-GaussFit.JPG'
  'media/ColocByCorrelate-GaussFit.jpg'
fatal: unable to checkout working tree
warning: Clone succeeded, but checkout failed.
You can inspect what was checked out with 'git status'
and retry the checkout with 'git checkout -f HEAD'

Handle missing page descriptions in search

We don't have descriptions for the pages converted to mediawiki. We should remove the dummy text there and Just grab the beginning of the text of the page and display it in the search.

Generalize styling of related plugins (ex: SNT)

The SNT page has an intro box with links to related sections. This should be standardized, perhaps through front matter?

Conversion: Titles with colon break github page

The github page build is failing because of pages with colons in the title: https://github.com/imagej/imagej.github.io/runs/846248509 I will exclude them from the autoconversion for now.

Logo link should go to ImageJ2 (Home, about...) - NOT fiji

Ensure there are no broken links, and automate the check

The script _bin/broken-links.sh prints out links that it detects as broken. But it needs updating to handle additional cases:

• /ij/* – proxied mirror.imagej.net content – needs update to serve from /ij and redirect old links from the root where feasible (e.g. /macros)
• Other repos in this org: /presentations, /workshops, /tutorials, /list-of-update-sites, others?

List of known observed weirdness so far:

• BigDataServer: INFO__ are linkish, but are surrounded in backticks. These should be fixed, and other instances of backtick-mangling should be checked for.
• Some MediaWiki-style links got escaped with backslashes—\[link title\]—I fixed many of them but would be good to double check there aren't any remaining.
• (Category_Segmentation) (and similar) links—and _bin/broken-links.sh does not find them.

Once we have a robust dead link checker, we also need to hook it up to an action to check when links break.

See also #55, #63 (IJ1 page renames), #66

Convert mediawiki namespace links

MediaWiki category-style links no longer work. Each link needs to be replaced with a link to the appropriate equivalent page, e.g. [:Category:plugins] --> https://imagej.github.io/plugin_grid (or similar)

Known namespaces:

• [:Category:...]
• [File:...]
• [Special:...]
• User:
• Template:

Improve sidebar placement

There are (at least) three kinds of sidebars:

1. Table of contents
2. Menus (e.g. Development menu)
3. Plugin/component info boxes

All of these should be located in the left and/or right margins, to avoid displacing the main narrative text.

Here is a rough first cut at some CSS rules that start going in the direction I have in mind:

.toc {
position: absolute;
left: 0;
font-size: 0.75em;
width: 240px;
DELETE -- margin-right
DELETE -- max-width
DELETE -- margin-bottom
}

.container {
margin: 0 200px; // the 200px is left & right margin... for sidebars
DELETE? -- max-width: calc(100% - 4em);
DELETE? -- width: 60em;
}

#content {
 // check this!
}
.page-content {
 // check this!
}

#info-box {
DELETE -- float: right;
DELETE -- min-width: 500px;
position: absolute;
right: 0;
width: 240px;
font-size: 0.75em;
}

.table-info { // main.css:3237
  DELETE -- width: 80%;
  DELETE -- margin: 0 10%;
}

.main { // main.css:4007 (and main.css:3483)
padding: 0;
}

Maybe we can use absolute positioning inside relative positioning or similar tricks to put multiple sidebars vertically sequentially without overlapping?

One problem is that when screen width gets narrow (e.g. mobile phones), the margins disappear, and these sidebars will need to become sandwich menus or else "pop in" to the main column. Further development and experimentation needed to develop a good set of CSS rules.

If no one else is comfortable doing this while I'm away, I'll work on it later this fall.

Use shorter titles for some pages

Some pages have a short-name redirect to a full-name page. For example, Batch redirects to Batch_Processing. But this was an artifact of the fact that MediaWiki conflates page title with URL. Now that we are using Jekyll, we can have a short URL with a full (non-matching) page title. And we should. The question is: for which pages?

This issue is an attempt to document easy places to prefer the short URL with long page title. I ran the following command:

git grep 'REDIRECT *\[*' | sed 's/^\([^:]*\).md:.*REDIRECT\ \[*\([^]]*\)\].*/\1 % \2/' | grep '^[^ _%]* % [^ _]*[ _]' | sed 's/\\//g' | sed 's/ % / <- /'

This searches through all the REDIRECT and #REDIRECT statements of the stub pages, extracts the string indicating redirect destination, then filters down to only redirects which have a single-word source going to a multi-word destination.

Here is the list:

• 3D ⬅️ Visualization#Visualization_of_Volumetric_Image_Data
• AnomalousDiffusionFilters ⬅️ Anomalous_Diffusion_Filters
• Application ⬅️ Getting_started
• Asd ⬅️ Stochastic_Denoising
• BIG ⬅️ BIG_License
• BOM ⬅️ Architecture#Bill_of_Materials
• Batch ⬅️ Batch_Processing
• BeanShell ⬅️ BeanShell_Scripting
• Beanshell ⬅️ BeanShell_Scripting
• Bugs ⬅️ Report_a_Bug
• CC0 ⬅️ Public_Domain
• CLAHE ⬅️ Enhance_Local_Contrast_(CLAHE)
• CLI ⬅️ Developing_ImageJ_on_the_command_line
• Clojure ⬅️ Clojure_Scripting
• Code ⬅️ Source_code
• Coloc2 ⬅️ Coloc_2
• Colocalization ⬅️ Colocalization_Analysis
• ColocalizationAnalysis ⬅️ Colocalization_Analysis
• Common ⬅️ ImageJ_Common
• Concatenate ⬅️ Stack_Manipulation
• Customize ⬅️ Update_Sites
• DS4H ⬅️ DS4H_Image_Alignment
• Daltonize ⬅️ Simulate_Color_Blindness
• De-Interleave ⬅️ Stack_Manipulation
• Deinterleave ⬅️ Stack_Manipulation
• DetectInformationLoss ⬅️ Detect_Information_Loss
• Dialog ⬅️ Generic_dialog
• Eclipse ⬅️ Developing_ImageJ_in_Eclipse
• Events ⬅️ Upcoming_Events
• FAQ ⬅️ Frequently_Asked_Questions
• FFMPEG ⬅️ Links#Movie_support
• Fake ⬅️ Fiji_Build_System
• Faq ⬅️ Frequently_Asked_Questions
• GUI ⬅️ Graphical_user_interface
• GenericDialog ⬅️ Generic_dialog
• Groovy ⬅️ Groovy_Scripting
• Guide ⬅️ User_Guides
• Guides ⬅️ User_Guides
• IDEA ⬅️ Developing_ImageJ_in_IntelliJ_IDEA
• ImageJ-MATLAB ⬅️ MATLAB_Scripting
• ImageJ-Ops ⬅️ ImageJ_Ops
• ImageJ-matlab ⬅️ MATLAB_Scripting
• ImageStitching ⬅️ Image_Stitching
• ImgLib1 ⬅️ ImgLib1_(deprecated)
• Imglib ⬅️ ImgLib1_(deprecated)
• IntelliJ ⬅️ Developing_ImageJ_in_IntelliJ_IDEA
• Interleave ⬅️ Stack_Manipulation
• Issues ⬅️ Project_management#Issue_tracking
• JNA ⬅️ Developing_using_native_libraries#JNA
• JNI ⬅️ Developing_using_native_libraries#JNI
• JRuby ⬅️ JRuby_Scripting
• Java ⬅️ Writing_plugins
• Java3D ⬅️ Java_3D
• JavaOptions ⬅️ Java_Options
• JavaScript ⬅️ JavaScript_Scripting
• Javascript ⬅️ JavaScript_Scripting
• Jupyter ⬅️ Scijava_Jupyter_Kernel
• Jython ⬅️ Jython_Scripting
• KymographBuilder ⬅️ KymographBuilder_:_Yet_Another_Kymograph_Fiji_plugin
• LUMoS ⬅️ Spectral_Unmixing
• Learnathon ⬅️ Learnathon_2019
• Lifecycle ⬅️ Development_Lifecycle
• Lisp ⬅️ Clojure_Scripting
• MATLAB ⬅️ MATLAB_Scripting
• MBF ⬅️ MBF_Plugin_Collection
• MCVE ⬅️ Bug_reporting_best_practices
• MOPS ⬅️ Feature_Extraction
• MRIPerfusion ⬅️ MRI_Perfusion
• MS-ECS-2D ⬅️ MS-ECS-2D_update_site
• Macro ⬅️ Introduction_into_Macro_Programming
• Macros ⬅️ Introduction_into_Macro_Programming
• Manual ⬅️ User_Guides
• Manuals ⬅️ User_Guides
• Matlab ⬅️ MATLAB_Scripting
• Mission ⬅️ ImageJ2#ImageJ2.27s_Mission
• MosaicIA ⬅️ Interaction_Analysis
• Native ⬅️ Developing_using_native_libraries
• NetBeans ⬅️ Developing_ImageJ_in_NetBeans
• NoiseGenerator ⬅️ Noise_Generator
• NucleiWatershedSegmentation ⬅️ Nuclei_Watershed_Separation
• OPS ⬅️ 2014-04-04_-_Announcing_ImageJ_Ops
• Open-source ⬅️ Open_Source
• Ops ⬅️ ImageJ_Ops
• OpsDeconvolution ⬅️ Ops_Deconvolution
• Orientation ⬅️ BoneJ2#Orientation_.28WIP.29
• POM ⬅️ Architecture#Maven_component_structure
• POMs ⬅️ Architecture#Maven_component_structure
• Pi ⬅️ Raspberry_Pi
• Pitfalls ⬅️ IP_Principles
• Profiling ⬅️ Profiling_Java_Code
• Purify ⬅️ BoneJ2#Purify_.28WIP.29
• R ⬅️ Renjin_Scripting
• RATS ⬅️ RATS:_Robust_Automatic_Threshold_Selection
• RERO ⬅️ Philosophy#Release_early.2C_release_often
• RecViewer ⬅️ SNT:_Reconstruction_Viewer
• Recorder ⬅️ Introduction_into_Macro_Programming#The_recorder
• Release ⬅️ Development_Lifecycle
• Releases ⬅️ Development_Lifecycle
• Renjin ⬅️ Renjin_Scripting
• Reproducibility ⬅️ Architecture#Reproducible_builds
• Reproducible ⬅️ Architecture#Reproducible_builds
• Roadmap ⬅️ Project_management#Issue_tracking
• Ruby ⬅️ JRuby_Scripting
• SIFT ⬅️ Feature_Extraction
• SIOX ⬅️ SIOX:_Simple_Interactive_Object_Extraction
• SME ⬅️ SME_Projection
• Scala ⬅️ Scala_Scripting
• Script ⬅️ Using_the_Script_Editor
• Search ⬅️ Help#Searching_ImageJ_resources
• Server ⬅️ ImageJ_Server
• Services ⬅️ SciJava_Common#Services
• Shepp-Logan ⬅️ Shepp-Logan_Phantom
• SheppLogan ⬅️ Shepp-Logan_Phantom
• Sholl ⬅️ Sholl_Analysis
• SoC2009Application ⬅️ SoC_2009_Application
• SoC2009Ideas ⬅️ SoC_2009_Ideas
• SoC2009Template ⬅️ SoC_2009_Template
• SoC2010Ideas ⬅️ SoC_2010_Ideas
• Source ⬅️ Source_code
• SpatialCalibration ⬅️ Spatial_Calibration
• SplineDeformationGenerator ⬅️ Spline_Deformation_Generator
• Stitching ⬅️ Image_Stitching
• Strahler ⬅️ Strahler_Analysis
• TWS ⬅️ Trainable_Weka_Segmentation
• Team ⬅️ Governance#SciJava_team_roles
• Tools ⬅️ Project_management
• Unlicense ⬅️ Public_Domain
• VCell ⬅️ Virtual_Cell
• VIB ⬅️ VIB_Protocol
• VirtualCell ⬅️ Virtual_Cell
• Wiki ⬅️ Contributing#This_web_site
• YouTube ⬅️ YouTube_Channel

Looking through it, there are some good suggestions, and some bad ones. We ultimately still need to make a manual judgment for each page, whether to keep the longer title or the shorter one. But hopefully this is a good start—it's 132 entries instead of 642!

Make overlay images

It would be cool to overlay put some code on the developer page - something with @Parameters

Not sure if there's a nice equivalent for users..

could either overlay the ImageJ logo onto it, or put it as the background for one of the sections, or tile the site background.. lots of options..

Support oneboxed links

Discourse reads Open Graph and oEmbed metadata from pages to generate oneboxed links. To support that, I believe all we need to do is add some meta tags to our page layout here. See this gist for an example.

Ensure old URLs all redirect appropriately

We can keep imagej.net pointed at a LOCI server, and use Proxy/ProxyReverse to forward requests on to GitHub, same as we do with fiji.sc. That way, we can add Apache redirect rules for previous pages that have moved. This will be particularly important for extensions. We may also want to downcase all the links, since needing to put capital letters for things really throws people off (@elevans: is GitHub Pages case sensitive? If so: is there a way to make it case insensitive? Would be much nicer if so.)

Fix table conversion

Many tables become unusable during conversion with a good part of a table being completely gone or rows not matching up any more. I have not looked into it and I have not been able to spot a pattern, but here is an example:

Old: https://imagej.net/Distribution
New: http://imagej.github.io/pages/Distribution

about/usage URL is out-of-date

The url on the usage page leads to a page that no longer exists:

https://juglab.mpi-cbg.de/matomo/

Markdown preview fine but render failing?

Hi Guys,
I've been looking at the SNT pages, and have a question. Consider, e.g., https://imagej.github.io/SNT__Manual

It renders like this:

So, when I try to edit it (to fix the rendering issues), the page renders the markdown perfectly fine in the Github previewer:

What is the best way to tackle this: Use a more strict markdown previewer? (Which one?) Use jekyll?

Review _includes logic for DRYness/simplicity

For example, there are some captures in _includes that might be unnecessary. E.g. macos captures include.content into info_content, then recapitulates it below. Maybe to make markdown=1 work as desired, but further testing needed.

Add redirects

We should add redirects for imagej.github.io:

• use.imagej.net
• user.imagej.net
• imagej.net
• imagej.net/Use

and for imagej.github.io/develop.html:

• develop.imagej.net
• developer.imagej.net
• devel.imagej.net
• imagej.net/Develop

Improve the website's search functionality

Right now the search functionality is purely client-side, which I personally love. However, @turekg has developed a more badass server-side search as part of an effort to better index our community's public conversations on Gitter, which could also be utilized for imagej.net content and more. The goal is to fully replace the rather cheesy https://search.imagej.net site with a unified and integrated search from imagej.net itself.

This is not an immediate goal before we cut over from MediaWiki, but is a strong "would be awesome" goal we want to pursue soon, depending on how the quality of the initial client-side search ends up being once the existing content has been migrated (see #11).

Front page ham menu is broken

index.md's hamburger menu is not fully appearing when activated. At first glance, it seems to be a z-level issue, due to a small grey box opening. This box ends when it hits the blue call-to-action section of the page. I've tried adjusting the z-level, as well tracking recent changes to nav-bar, home.html and relevant main.css code to ID potential issues, but have been unsuccessful in fixing the ham menu

Finalize the git history

We want the git history of the main branch to reflect the entire history of the ImageJ wiki from its MediaWiki days (same as we've done with https://github.com/openspim/openspim.github.io/). It's doable with git-remote-mediawiki backend. Concerns to watch out for:

• The main branch history will break when we force push, but we're still in the initial development phase right now, so that's OK. Any interested folks who've cloned it can force reset.
• The conversion of authors from MediaWiki names to real names + emails needs to be handled.
• Large binaries need to be excluded from the history.
• We want to split out the extensions (e.g. plugins) to their own repository, so we may need to be more clever and split the big MediaWiki history into two histories: one for extensions pages, and one for core pages. This will be more involved.

DokuWiki migration guide needs updating to cover GitHub Pages

The help/dokuwiki-migration guide describes MediaWiki. It needs updating for GitHub Pages, so that people can resume migrating their content from imagejdocu.list.lu to the new wiki.

Inconsistent rename for image with underscore in name

Pages like FLIMJ and Siam are missing images because underscores in some of the image name are not converted to spaces:

FLIMJ page:

Image list:

Figure out how to split up content (e.g. into extensions repository)

Because of the 1GB size limit we need a strategy for how to distribute content to not hit that limit.

The current idea is to create an extensions repository where all the non core pages would live. We need to analyze how much that helps and how to distinguish core from extension pages.

Fix wikipedia links

Wikipedia links need to be handled.

That's what they look like in mediawiki:

[[wikipedia:Application software|software application]]

.. that's the current conversion (at least when converting Development.mw, which produces a lot of HTML):

<a href="wikipedia:Application_software" title="wikilink">software application</a>

It should point to this URL: https://en.wikipedia.org/wiki/Application_software

Work toward removal of 'autogenerated: true' from all pages

This will be a community effort. Each page needs to have a human look at it, and declare its formatting good going forward. Then the autogenerated: true line can be removed for that page. Once they are all checked, this issue is resolved.

REST API search functionality (JSON)

Is there some way to get search results in JSON format already, e.g. via a REST API?
If not, maybe this can be added e.g. using https://github.com/riichard/jekyll-rest-api

(Related to #13.)

This would allow updating the built-in imagej.net search in scijava-search, see scijava/scijava-search#20.

Decide how breadcrumbs should work

As pointed out by @hinerm, the current way breadcrumbs are set up may need to be revised. Pending further discussion!

Conversion: Individually convert blacklisted pages

Probably all pages on this table need to be converted individually since they caused an error during mass conversion. The reason for each page (pandoc failing, python reader failing, liquid syntax error) and sometimes a more detailed explanation is included in the table.

It's probably the easiest to use the mass conversion script and adjust these two lines: Comment out convert_all() and uncomment convert_page('PAGE_NAME'). The script will delete all autogenerated pages before converting this one page, leading to a jekyll site that renders way faster than a site where all autogenerated pages exist. Once page in question is converted successfully, change the autogenerated: true line from the PAGE_NAME.md file header to something like autogenerated: edited and run mass_conversion with the convert_all() line again. The page can then be removed from the blacklist, it will not be converted again since the converted file already exists and doesn't have the autogenerated: true line.

Example code missing on imagej.github.io

Hi all,

I just discovered an important difference between the new website on imagej.github.io and imagej.net: Example code is missing as shown here:

And here are the links to the two pages:

http://imagej.github.io/ImgLib2_Examples

https://imagej.net/ImgLib2_Examples

Thanks everyone involved for working on this btw. the new website is a big step forward!

Cheers,
Robert

Add mailman archives (pipermail, mailman/listinfo, mailman/admin)

The old imagej-devel mailing list archives need to be preserved. Easiest way would be to simply commit all the static HTML content from the archives into this repository, along with everything else. We should also consider whether to commit imagej-bugs and imagej-builds, but size may be an issue:

64M     imagej-bugs/
243M    imagej-builds/
108M    imagej-devel/

Javascript magic for component-stats include

The component-stats include should reach out to maven.scijava.org to extract needed metadata for the component.

We can write JavaScript for this. The URL to fetch is:

https://maven.scijava.org/service/local/artifact/maven/redirect?r=public&g=org.scijava&a=scijava-common&v=RELEASE&e=pom

Where org.scijava is the requested groupId and scijava-common is the requested artifactId. This should work regardless of whether the component is published on Central / OSS Sonatype, or SciJava Maven, or somewhere else proxied by the SciJava Nexus.

Then, it's just a matter of feeding the downloaded XML into a javascript XML parser and extracting the right values. Hopefully javascript has easy-to-use lightweight xpath expression support, which can easily grab all the needed fields for the component-stats box. Essentially, the logic from this code will need to be recast into javascript.

Add toc title and "-" dashes for child menu items

via assets/js/jquery.toc.js

Add a table of contents title: "Table of Contents"
Add "-" dashes to children of parent menu items for readability

Sort all pages into concise subdirs, and use standard-web-naming

All pages should be classified into subdirs. As of this writing, there are a few pages still with the MediaWikiNaming directly in the _pages folder. We need to classify these.

And finalize where things currently live. Some existing structure is questionable, including:

• tutorials/* vs scripting/examples/* scripts (needs unification)
• /update-sites should move to /help or /learn to avoid confusion with /sites (which is a section for pages about each update site people care to document on the wiki)

Add fancy transitions

These are really nice but I couldn't figure out how to repurpose the nav bar to use the transitions

Fix deprecated MathJax usage

Browser says:

WARNING: cdn.mathjax.org has been retired. Check https://www.mathjax.org/cdn-shutting-down/ for migration tips.

Update the documentation for update sites

We need to update the docs surrounding update sites to recommend people (at least for now) start a forum topic asking for update sites to be created, plus granting write permission to the needed user(s). MediaWiki-specific instructions surrounding update sites need to be removed from the documentation.

Consolidate Similar Templates

Conversion: Handle Conference pages

We probably need a layout for pages like Conference-2006.mw:

{{Conference
| title=ImageJ 2006 User & Developer Conference
| section=1st ImageJ User & Developer Conference
| dates=18 - 19 May 2006
| image=Imagej-conference-2006.jpg
| location=CRP Henri Tudor in Luxembourg
| link=http://imagejconf.tudor.lu/archive/imagej-user-and-developer-conference-2006
}}

Nothing of the content of the file is currently rendered on the generated page.

Update old and/or redirected links

I have already fixed many of these, but a few remain:

• fiji.sc (check case by case)
• fiji.sc/downloads ➡️ downloads.imagej.net/fiji
• fiji.sc/git / git.imagej.net / fiji.sc/gitweb.cgi ➡️ {% include github ... %}
• forum.imagej.net ➡️ forum.image.sc
• maven.imagej.net ➡️ maven.scijava.org
• fiji.sc/javadoc / javadoc.imagej.net ➡️ javadoc.scijava.org
• jenkins.imagej.net ➡️ ???
• and in general look for all links to imagej.net, fiji.sc, scijava.org, scif.io, etc., and ensure they are up-to-date

See also #66.