QuickFigures: Any Testing Help?

Greg1 · March 19, 2021, 6:08pm

Hello Everyone,
I created QuickFigures, a Fiji/ImageJ plugin for creating figures from microscopy images. I would like some help testing out the most recent version. A tester would need to confirm that 1) They can understand both the video tutorials and the user guide on github, 2) They can install and use the plugin and use the features shown in the tutorials and user guide, 3) let me know if they encounter any bugs. Links to the bioRxiv manuscript, user guide, video tutorial and github page are below.

Please contact me if you are interested in helping. Even something as small as finding a single type-o would be a favor.

github.com

grishkam/QuickFigures/blob/ae017cabcd347a826e62ae91f3c50d737603b990/UserGuide/User Guide.md

# QuickFigures User Guide  
By Gregory Mazo  
Publications involving fluorescent microscopy generally contain many panels with split channels, merged images, scale bars and label text. Similar layouts of panels are used when displaying photographs, electron micrographs and other forms of images. Assembling and editing these figures with even spacing, consistent font, text position, accurate scale bars and other features can be tedious and time consuming. In order to save time and streamline the process I have created a toolset and ImageJ Plugin called QuickFigures. This user guide covers the key features. Please reach out to me if you have any questions or recommendations.  


## Section 1: Install 
### Install instructions
### Fiji Install: 

#### Step 1: update Fiji (if not already up to date)
-	Go the Help menu and select **'Update'**
-	Apply changes to make sure your Fiji is up to date
-	Restart Fiji

#### Step 2: Install QuickFigures
-	Go the 'Help->Update' menu item again
-	After a moment, Fiji will tell you that you are up to date
-	In the next dialog window click **Manage Update Sites**
-	QuickFigures will appear in the update site list
-	Check QuickFigures

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Thanks a lot,
Greg

At the moment, I am focused on finding people to do manual testing without needing to look at nor understand any computer code. However, if you would like to do anything beyond that, I would be grateful to hear it.

biovoxxel · March 20, 2021, 7:52pm

Just started playing around to test a few things. I am just like…
Already a FAN

What I like most is that saving as SVG (other options not tested yet) preserves the original image quality and resolution.
I recently implemented something similar, but by far not as versatile as QuickFigures.

This finally and hopefully enables more people to create loss-free and high quality publication figures without over-interpolating or in resolution-destructive ways.

After finishing testing, I am happy to

give more detailed feedback
promote your tool among young scientists if this is in your interest and desired.

Thank you very much for sharing such a great tool.

Greg1 · March 21, 2021, 12:03am

Thank you so much for taking a look at it! More detailed feedback would help a lot. Feedback on the user guide and videos would also be helpful.

samjlord · March 22, 2021, 11:34pm

Hi Greg,

I’d be interested in helping test. I played around with QuickFigures when the preprint first came out and I’d be happy to try with the latest version.

Sam

Greg1 · March 22, 2021, 11:56pm

Thanks so much Sam,
Message me when you have your feedback ready.

All the best,
Greg

camlloyd · March 23, 2021, 1:58pm

Hello @Greg1,

Thank you for creating QuickFigures. I wish it existed a long time ago.

A few points (my opinion):

The installation instructions were simple to follow and getting started was easy using the update site.

The README could be even easier to read if the links were formatted differently - perhaps like this:

1. Installing QuickFigures

Download the latest release on GitHub here.

Screenshot 2021-03-23 at 13.42.29 Sorry! PR to follow…

Finally, is it possible to move Quick Figures under the Plugins menu?

This may make it slightly less Quick, but it is still easy to access using the search bar.

Thanks!

Greg1 · March 25, 2021, 4:38am

Thanks for the input Cameron,
Improvements to the readme file and type-O fix will come with the next update.
I will put the QuickFigures menu in the plugins menu. However, for a time I will keep the menu in both locations to avoid confusing existing users.

Greg1 · March 26, 2021, 2:04pm

I implemented Cameron’s suggestions.
I am still seeking more input.

Thanks again,
Greg

RemyB · March 29, 2021, 1:35pm

Hello Greg,

I have tested QuickFigures and I love it. It is really a great tool. Thank you so much for your time and effort for making this fantastic plug-in.

I have just some small comments for now concerning the usage and interface.

Is it possible to have the layout size in centimeters and not in inches? (We don’t use so much inches in Europe and it may help to have an option to change all unit to the metric system).

Also, when creating an inset with the inset tool, would it be possible to add a keyboard shortcut that we press at the same time as the mouse to allow to draw the inset as a square shape?

I maybe missed it, but is there a way to quickly show the drawn inset on each channels and on merge?

Thank you so much again for your great plug-in.

Bests

Remy

biovoxxel · March 29, 2021, 1:51pm

I had similar things in mind. So, I might add to @RemyB’s requests:

I second the metric system request
square-lock for inset selections.
I couldn’t find a solution for the problem, that when I draw a region of interest to create an inset, to get the latter resized to fit the original image width. Is there a possibility to make e.g. the inset width the same as the base images the inset came from. Meaning that the insets are scaled up to have the same “size” (in terms of column width) that the originals in the corresponding layout?
For me zooming in need the “=” sign, which is a little bit odd. zooming out works with “minus”, so the latter is fine. Could this be + and - as a more intuitive zooming key board combination? Even better would be zooming via the [mouse wheel] or a combination of [Ctrl] + [Mouse wheel].

Greg1 · March 29, 2021, 4:39pm

Thanks guys,
These are great ideas. I will be able work on them after I have finished the
manuscript revisions. Although I might implement some of the simpler ones earlier.
An option to switch to the metric system is definitely going to happen.

I really appreciate the help,
Greg

Greg1 · April 5, 2021, 2:29am

Hi Everyone,
If anyone detects any bugs while using QuickFigures it would help me out if they let me know. I have fixed bugs that I have found myself (on both Windows and Mac). However, if anyone notices a problem that slipped past me or is specific to their computer, I would really appreciate it if they told me.
Specifically, there is one bug that someone observed several months ago using an older version of QuickFigures that I could not reproduce at all. I have access to several computers but have never see this issue on any of them: “There is some problem with the ‘Object Tools’ frame. It needs to be restarted manually by the user as icons and functions get lost. This happens quite frequently”. Does anyone see something like this happen on their own computer with a recent QuickFgures?

Thanks everyone for all of the input,
Greg

Greg1 · April 12, 2021, 6:06pm

Hello Jan,
I have added options to switch to metric rulers, square lock insets, scale insets to fit parent panel width, and [Ctrl]+ [Mouse Wheel] to zoom. Check out the user guide for details. I will put out an announcement later.

Best,
G

biovoxxel · April 13, 2021, 7:24am

Thanks @Greg1,

very very nice! Kudos to you. Zooming is now a lot more intuitive.
At some points I still need to get a little bit more familiar with all the handling and possibilities. But it is definitely a milestone in figure creation tools.
I currently would still have one point from good scientific practice view: If an inset is made bigger (or an image smaller) its resolution in terms of amount of pixels should optimally not change. This is optically obviously only possible in vector graphics. If more pixels are added during size increase and then bilinear or bicubic interpolation is used, a higher artificial resolution impression is imposed in the image also leading to loss in detail and increased blurring and smudging effects.

First, if interpolation is used, I think bicubic should be preferred over bilinear one. As I read from the user guide QF is currently using bilinear. This should be easily adaptable or addable by creating a method for bicubic interpolation while scaling.

Original image in QF:

Inset with size increase (bilinear line artifacts are visible and blurring/smudging ocurrs):

Second, best would be no interpolation and just increasing the size of the square representing the original pixel. I assume the images on the figure panel are treated as vector graphic. If this is the case, avoiding interpolation is perfectly applicable. If my assumptions are correct it would be cool to have an option switching between “no” and “bicubic” interpolation and “no interpolation” being the default. But I don’t know if and how simple that would be to implement.
If the images are size increased by using the ImageJ intrinsic image scaling, then such an implementation will only be possible when inset resizing is locked to integer factor values (which is mostly not desired by the user)
I am happy to elaborate more on this, if my upper explanations were somewhat cryptic.
I will also have a look into the code these days and see if I can assist.

EDIT: here again in comparison (created in Inkscape):

Greg1 · April 13, 2021, 10:41am

It is definitely possible to add an option to switch interpolation types. Will add it after I finish revisions to the manuscript.
Thanks for the input,
G

Greg1 · April 13, 2021, 11:02am

Also, if you want to resize an image panel without changing the amount of pixels, there is already a way to do that. I should include a better discussion of scaling in the user guide.

semboko · April 13, 2021, 2:25pm

The plugin is just awesome, thanks a lot! Tested on my 4 channel z-stacks - everything works fine for me.

K_Taz · April 13, 2021, 4:13pm

Hi Greg,
Thank you for your tool, it’s fantastic!
In the latest update, I noticed that when I zoom in, I can’t move on the X or Y axis (I mean other than selecting the scrollbars). Am I missing something?
A cool way for me would be to move around like in imageJ by holding space and moving the displayed area with the mouse.
I hope you like the idea,
Thanks,
Kevin

Greg1 · April 14, 2021, 12:30am

Thanks Kevin,
Holding a button to move the display area is a good idea.
Also, you should not be able to scroll using the keyboard in the current version (not a bug).

biovoxxel · April 13, 2021, 5:16pm

I figured out that it is possible to scale an image with a factor and that keeps the pixels as in the original. However, using the inset creator tool (which is an amazing idea) QF seems to always use interpolation for the created insets. I did not figure out how to avoid that or if this is already possible.