Which Fiji plugins should be featured on the front page?

fiji
imagej
#21

Script Editor

writing scripts in multiple languages, includes features such as syntax highlighting, language specific templates, etc.

@albertcardona

6 Likes
#22

Thanks @ctrueden for adding the BioVoxxel Toolbox as well to the list.

A toolset providing a plugins and macros for flat-field background corrections, image filters, color coding of shape descriptors and several tools to process and analyze binary images such as the ‘Speckle Inspector’, ‘Binary Feature Extractor’ and an ‘Extended Particle Analyzer’ and a qualitative and quantitative evaluation tool for Fijis’ Auto Threshold methods. More information at the BioVoxxel Toolbox wiki page

8 Likes
#23

@biovoxxel
Can you add a little one-two sentence ‘blurb’ as well?

#24

TrackMate

An open and extensible platform for single-particle tracking.

@tinevez

8 Likes
#25

Edited it with a short description

1 Like
#26

Trainable Weka Segmentation

a collection of machine learning algorithms with a set of selected image features to produce pixel-based segmentations.

@iarganda

6 Likes
#27

BAR

Broadly Applicable Routines, containing macros, scripts, and plugins focused on data analysis, image annotation, and image segmentation.

@tferr

6 Likes
#28

BigDataViewer

re-slicing browser for terabyte-sized multi-view image sequences developed with multi-view light-sheet microscopy data in mind.

@tpietzsch

8 Likes
#29

MaMuT

combines TrackMate and BigDataViewer for browsing, annotating, and curating annotations for large image data.

MaMuT_WindowsInSync

@tinevez @tpietzsch

8 Likes
#30

@etarena Thanks a lot for working on these! :star2:

One thought: many of the descriptions begin with “A plugin that…” or similar language. I propose boiling down these blubs to the bare minimum (I am guilty myself of posting a too-long blurb for the Microscope Image Focus Quality Classifier). Here are some examples of what I am thinking:

  • CLIJ – Predefined OpenCL-based functions allowing you to run your workflows faster on any GPU.
  • Microscope Image Focus Quality Classifier – predict image focus quality and certainty patch by patch without any user-specified parameters
  • TrakEM2 – Morphological data mining, three-dimensional modeling, image stitching, registration, editing, and annotation
  • BigStitcher – Simple and efficient alignment of multi-tile and multi-angle image datasets
  • BoneJ – Bone image analysis, including tools for trabecular geometry and whole bone shape analysis
  • Coloc 2 – Pixel intensity correlation over space methods of Pearson, Manders, Costes, Li and more, for scatterplots, analysis, automatic thresholding and statistical significance testing
  • MorphoLibJ – Morphological filtering and reconstruction, watershed segmentation, 2D/3D measurements, and binary/label images utilities
  • SciView – 3D visualization and virtual reality capabilities for images and meshes
5 Likes
#31
  • BAR - Broadly Applicable Routines, containing macros, scripts, and plugins focused on data analysis, image annotation, and image segmentation.
  • BigDataViewer - re-slicing browser for terabyte-sized multi-view image sequences developed with multi-view light-sheet microscopy data in mind.
  • MaMuT - combines TrackMate and BigDataViewer for browsing, annotating, and curating annotations for large image data.
  • Script Editor - writing scripts in multiple languages, includes features such as syntax highlighting, language specific templates, etc.
  • TrackMate - an open and extensible platform for single-particle tracking.
  • Trainable Weka Segmentation - a collection of machine learning algorithms with a set of selected image features to produce pixel-based segmentations.
6 Likes
#32

This would be my short(er) version :wink:

BioVoxxel Toolbox - image filters, lighting correction, threshold tests and binary image modification algorithms and variable 2D object analysis tools.

2 Likes
#33

Thanks so much @etarena!!!

1 Like
#34

@malsf21

Hello! I think there should be enough plugins/tools with their short descriptions and images to get things started… just check the thread here and let me know if you need anything else.

#35

Wow this is great, thanks everyone! I’m working on it right now :slight_smile:

2 Likes
#36

Hi all, I’ve been working away on the plugins view. Here’s a super basic draft of what it’d look like with a few sample plugin blurbs. What are all of your thoughts?

4 Likes
#37

A huge leap forward compared to the old site. Thanks so much for working on it, @malsf21! :trophy: I’m in favor of merging ASAP. We can then add more plugins to the featured section.

Thoughts and questions:

  • What happens to the tabbed view of featured plugins when the number of tabs exceeds the space? Does it elegantly handle the number of plugins we want to feature? If not, how best to address it?
  • The embedded Twitter feed is cramped. Is there a better way? E.g. can we use a more compact Twitter widget there?
  • I’d like to add a “Read more” button to the Licensing section that goes to https://imagej.net/Licensing.
  • The Contriibutors section’s blurb about project maintenance should be updated to include MPI-CBG / CSBD as well now. I’m happy to do this as soon as the dust settles on this revamp.
2 Likes
#38

Yeah, I had already thought about this for a bit. The tabs look subpar, though we have a few options:

  • (my personal favourite) feature at most 5 plugins at a time, that change on page load
  • have horizontal scrolling for the tabs section
  • switch to a dropdown or some other container

Do you feel partial to any specific implementation?

The widget itself is the only supported Twitter timeline embed, however I can add vertical/horizontal margins or padding, and give it its own block of content instead of making it share a row with Contributing. Is that what you were thinking of?

Done!

Gotcha, I’ll leave that to you then!

Once those first two points are done, I feel like it’s ready to merge too! I’ll also likely quickly add a README that discusses the libraries we use for the site, and some basic information about how it works.

2 Likes
#39

Is there a reason you don’t like classic Bootstrap carousels? IMHO it handles more pages at a time elegantly.

Otherwise, I agree with you that featuring 5 random ones at a time would be totally fine.

That’s how the current site does it, and it bothers me that way too. :stuck_out_tongue_winking_eye: It just feels like a lot of emphasis on the Twitter feed when it’s full width, so I’d rather not.

Upon reflection, I think a big reason the current 50% width version feels cramped is that it is not tall enough. My idea would be to make it occupy the right half of the page from “Contributors” all the way down through “Citing Fiji”. For the Partnered Projects, the icons can be reduced in size to accommodate that. And when the page width gets small enough (e.g. on mobile), it’s fine for the Twitter feed to become full width as it does currently. Definitely open to other suggestions though!

Thanks again for all your efforts on this!

1 Like
#40

Personally, I’m not a huge fan of Bootstrap’s carousels - I feel like they’re hard to use on mobile and rather jarring (especially as the page height will change dynamically when differently-sized images are automatically cycled through). However, if the carousel seems like the best option, I’m fine with implementing that too, as it wouldn’t be too hard for me to change any of the tab code. What are your thoughts?

Good suggestion, I pushed what that might look like to my fork. Let me know how you think it looks.