laulauthom / fiji-qualiannotations Goto Github PK

Problem with non-rectangular ROIs and if one mix and match ROI shapes
Ex: annotate a rectangle and then a circle -> not the same number of coordinates

Or a single column "ROI coordinates" with predefined formatting explained in the doc

This would enable tagging phenotypes not previously encountered.

With multiple classes, hard to figure out which shortcut for which category
Either use a pop up balloon to give a hint about the shortcut or directly put it in the button label

The full citation is taking some space, better move to it to a dedicated plugin.

• add a dropdown to select the dimensions to progress ?
  Check how this is done in imageJ

Observed once with ImageJ 1.52p.
Updating ImageJ (Help > Update ImageJ) to version 1.52v solves the issue.

Continuing an annotation from an existing table could be made easier by giving the possibility to generate the category choices from an existing table.

Give this option in the pre-annotation window ?
Button "Load from file" or "...from current table"

• Test on a virtual machine ?
• Test the other plugins
• Test on Linux too

This is a known Fiji issue, that does not prevent the execution of the plugin.
It should be fixed in the next ImageJ-launcher release.
See https://github.com/multi-template-matching/MultiTemplateMatching-Fiji/wiki/Issues for the current workaround solution.

Just check for open images with window manager and display a message and stop execution upon button click if no images

For the annotation of images with different image sizes, annotating hyperstack is not straightforward.
One could give the option to annotate one image at a time by annotating from a directory on disk.

Ask for "stack" or "from disk" in a dedicated option window before generating the GUI ?

Currently annotating the same image or ROI will result in duplicate entries in the table.
Give the option to replace existing entries.

This means checking some column values to see if they contain the value which is about to be appended.
The branch overwrite-bruteforce-search adds a checkbox "Overwriting existing" and a function to find existing rows provided a folder, image and optional slice and roi identifier.

Problem: when measurement is selected the analyzer automatically adds to the result table
From there possible solutions:

• make the analyzer write to another table with a unique ro, read this row into a dictionary and close the table
• check if Measure: read last row, delete last row, replace existing row
• modify the Analyzer class so that it returns the measurement into a variable (but then not available for current version of ImageJ/Fiji)

Rather for the article but currently all post-processing is done in KNIME.
One example in ImageJ/Fiji would be appreciated, try the sunburst plot in ImageJ/Fiji with JFreeChart ?

Suggested by reviewers (see article page on F1000)

Seems that it did not open the page in a browser on Mac
See if it's an issue in the BrowserLauncher class
https://imagej.nih.gov/ij/developer/api/ij/plugin/BrowserLauncher.html