ScientiFig: Frequently Asked Questions (FAQ)
How do I get started?
Please have a look at the video tutorials on the previous page
What is ScientiFig?
ScientiFig is a free software that allows you to create, format and/or reformat scientific figures
How can I launch the software?
-for beginners: just double click on launcher.jar (if you manipulate big images, go for that).
-for beginners2: install SF as an ImageJ/FIJI plugin, see the section “How do I use SF as an ImageJ/FIJI plugin?”
-for beginners: double click on launcher.jar
-for advanced users: open a command line and type in something like (Xmx1024m means 1024 Mb RAM, change this number to meet your requirements): java -jar -Xmx1024m ScientiFig.jar
How do I use SF as an ImageJ/FIJI plugin?
-SF is ImageJ/FIJI friendly. Unzip the zip file you just downloaded in a destination folder and then copy this destination folder to the ImageJ/FIJI "plugins" directory. Once this is done open ImageJ/FIJI, click on the "plugins" menu and select ScientiFig.
What are the requirements?
SF works on Linux, Mac (Mac intel only) and Windows. It is recommended you run it on a computer with at least 1512Mb of RAM.
In which language is SF coded?
-SF is coded in Java (like ImageJ).
Which image formats are supported?
-Input formats: svg (svg import is still work in progress), jpg, yf5m (SF default output format), png, bmp, tga, tif
-Output Formats: svg (preferred ouput format for publications), png (preferred output format for office documents), tif, jpg, ppt
How do I add images to the software?
-solution #1 (simplest): just drop your images onto the "image list" (where the mouse pointer is).
-solution #2: click on menu>Import
I have created a montage/Figure and I would like to export it as a raster or a vector image
-Click on File>Export as... and then select the format you like
How do I save ?
-Just click on save or Save as. A ".yf5m” file will be generated; this file contains anything SF needs to rebuild your figure.
The journal I'm interested in is not available, what can I do?
-SF ships with a limited number of journals styles, but allows you to create a quasi-infinite number of styles. To create a new style just click on "journal">"create new journal style"
Fill in all the necessary parameters and click ok.
Your style is now available in the journal combo just below the menu bar.
Please don’t hesitate to contribute a style, you will be acknowledged for it (scientifig@gmail.com).
The journal style in SF is obsolete, what can I do?
-SF allows you to edit a style. Select a journal style in the journal combo below the menu bar
then click on journal>edit journal style in the menu bar.
Change the obsolete parameters, then click on ok, your style is now changed (you may just need to reapply it).
I have created a figure/montage, I want to use it for a publication which export format do you recommend?
-I strongly recommend the svg format. These files can be opened using your favorite vector graphics editors (Adobe Illustrator, Inkscape (free),...). From these vector graphics editors you can export to any format you like such as tif (at any resolution/dpi you want), to pdf, ... Otherwise if you really want a raster format I recommend the tif format with a high resolution (>=300 dpi)
How can I change the lettering of my montages/figures ?
-above the montage/figure list there is a small textarea that allows you to write one letter, put here the first letter of your figure then click on "update" and your letters will be changed.
What are the advantages of the svg format?
-svg is a vector graphics format. The position and size of images is more precise in this type of images than in raster images (png, jpg, tif). In addition, in svg files, images and texts are objects that can be edited, moved or deleted.
I need a figure with a 300 or 500dpi resolution, how can I get that?
-new!: you can directly export as tif or png at any dpi you want (the dpi settings are in the save dialog)
-export your figure as svg, open the generated file using a vector graphics editor (Inkscape, Illustrator, ...) and click on "export as tif", then specify the dpi when prompted.
I have created a figure that I want to add to my office presentation, which format do you recommend?
-I strongly recommend the png format, because it is a lossless compressed raster format and allows background transparency.
Can I change the order of images in a montage/the order of rows in a figure?
-yes, you can. Just above the "montage and figure lists" there are arrows pointing up or down, click on the position of your selected image/row will be changed.
I used ScientiFig a lot and I need a reference
Please cite https://grr.gred-clermont.fr/labmirouse/software/
Can I help ?
If you want to contribute a journal style or report a bug please contact scientifig@gmail.com
My montage was 3X2 (3 cols/ 2rows) I want to make it 2X3 can I do that?
-yes, just click on the "format" button above the "Montage List"
My montage was in meander order I want it in comb order can I change the order?
-yes, just click on the "format" button above the "Montage List" and select comb instead of meander.
I would like to move an image with my mouse can I do it?
-no, SF doesn't allow you perturb the computer calculated position of images and texts. Dragging capabilities of the software have been disabled. However you can export your montage/figure as svg and open it using a vector graphics editor and move anything you like there.
Can I import images from ImageJ/FIJI ?
-if you use SF as an ImageJ/FIJI plugin: just select an image in ImageJ/FIJI and click on the "import from ImageJ" button, your ImageJ image will be added to SF "image list".
-if you use SF as a stand-alone: click on the "import from ImageJ" button. ImageJ will pop. Open an image in ImageJ and click on import from ImageJ again; your image will be added to the list.
SF complains about a missing font, what can I do?
-it means the journal style you chose is probably using fonts that are not installed on your system. One solution is to install the font on your system, I can’t help you with that.
-Of note: if the missing font is Helvetica (Helvetica is a patented font that is not installed by default on Windows/Linux systems), then be aware that it can be substituted by the Arial Font (only experts can make the difference between these two fonts). So just create your figure using the Arial font and export your figure/montage as an svg file. The open it using your favorite vector graphics editor (Inkscape, Adobe Illustrator, …) and try to substitute Arial by Helvetica there (the font might also be absent in these softwares however).
What libraries are used by SF?
-SF includes the "batik" library developed by the Apache Software Foundation (http://www.apache.org/) to import/export vector images
-SF includes the Apache "POI" library to export as ppt
-SF includes the ImageJ library (PD library donated by Wayne Rasband) to export images as tif and to import image informations (such as pixel size) from ImageJ images
-the SF plugin FiguR may use the Rsession library (BSD, µlabs, https://sites.google.com/site/mulabsltd/products/rsession to send commands to the R software) if you include graphs in your figures.
I love SF icons, are they free ?
-Have a look at the license file and you will have all the necessary informations about the icons and where to get them.
Can I open svg files with ImageJ/FIJI?
-to my knowledge you can't (let me know if I'm wrong). ImageJ only supports raster images.
there are weird icons in the soft and I don't know what they mean
-if you put your mouse over a button and stay long enough, a tooltip will pop and give you more informations about what the button does.
I would like to undo/redo changes
-to activate undo/redo click on the "edit" menu and select "preferences". You can set there the number of undos/redos allowed. NB: activating undo/redo will slow down the software (a bit).
How can I remove all the letters
-remove the letter (or put a space) in the letter textarea then click update and your letters will disappear.
How can I create a montage?
-import images in the “Image List” then click on the “arrow” or on the “auto” button on the right of the image list. Fill in the montage parameters and you’re done.
Can I add images to an existing montage?
-you can add images to an existing montage, just select the montage in the "montage list", select the image(s) you want to add in your "image List" and click the "+" button (see mouse position).
The editor and/or the reviewers did not see the beauty/novelty of my work and rejected my paper, I would like to submit my figures to another journal that uses different fonts and figure sizes, do I have to redo everything?
-no. Just reopen your yf5m file then select your new journal style
or create one if it does not exist (see FAQ on how to create a new journal style). Finally click on the Montages/Figures>Apply the Selected Journal Style To All components.
By the way you can do the same for figure size (button just below).
-As an alternative select all the rows in the “Figure List” and then select a journal style, the selected style will be applied to all selected rows.
How can I create a Figure?
first you have to create montages, once this is done, click on the “prepare figure” panel.
-to add a row click select a montage then click on the arrow
-or to add another column to this row click on +
-to set all the component of the row to the same height click on same height
Sometimes when I create a figure one of the montages in a row seems to be a bit smaller than its immediate neighbor, what can I do?
solution #1: try selecting the row and click on "same height" (one or many times) it might solve the problem
-solution #2: The problem should not be present (or not visible) if you export the figure as svg. Indeed this problem is due to raster rounding errors, there is no solution.
I have a row that contains n montages and they all have different heights, what can I do?
-click on the "same height" button
Can I export montages/figure from SF to ImageJ/FIJI?
-yes, just click on File>Export to ImageJ
I have created a figure but all the rows in it have different width, how can I fix that?
-Example:
-solution #1 (slow): select each row individually in the "Figure List" and set its size in cm or in pixels (the size spinners can be found just below the menu bar)
-solution #2 (fast): specify a size in pixels or in cm.
then click on Figure/Montages>Apply selected Width in cm/px to all Components
yf5m what does this extension stand for, can I open it using other softwares ?
-during its development SF had several code names, such as “burgerfig”, "figure Assistant" and "your figure in 5 minutes" yf5m, I kept this last name as a file extension since “.sf” is already attributed. A yf5m file is just a serialized java object that contains all the necessary info to rebuild your figure, as a conclusion it cannot be opened by other softwares.
It doesn’t run on my Mac
If your Mac is not an “intel Mac” there is nothing I can do. If you have a “Mac Intel”, please follow the instructions:
Go to applications>utilities and look for file called “java preferences”. Tick java 1.6 (or 6.0) wherever it is possible and make sure that you drag the ticked java 1.6 to the top of each list. Relaunch ScientiFig.
It doesn’t run on my PC
Please install the last version of java (click here) on your PC, once the installation is done ScientiFig should work.
How do I launch SF from the command line ?
- open a command line (see the section how do I open the command line) and type in:
java -jar -Xmx1024m ScientiFig.jar
NB -Xmx1024m means that up to 1024 Mb of RAM can be allocated to the JVM.
ScientiFig crashed/I have discovered a bug
The most common source of error is “a not enough memory”/”java heap space” error and unfortunately I can't fix these errors so please don't report them to me. These errors occur because the JVM was not assigned enough RAM. To avoid this type of error you have to launch SF from the command line and specify how much memory should be used by SF: please see the section "How do I launch SF from the command line?". As an alternative create smaller figures montages and combine them using your favorite graphics editor maybe it'll have enough memory to create your figure.
How do I open a terminal?
-On PC: Press the “Windows” key + R. The “Windows” key is located between the “Alt” and “Ctrl” keys on your keyboard. A window will appear; type in “cmd” and press “Enter”.
-On Mac: Go to applications>utilities and then double click on “Terminal”.
How do I know which version of java is installed by default on my computer ?
-Open a terminal and type in “java -version”, this command will tell you which version of java you are using.
How much do I have to pay to use this software?
-Nothing, SF is free and that's the beauty of it.
What happens when I reach the end of the FAQ?
-Nothing. But I would like to thank you for taking time to read the FAQ entirely, I really appreciate. I hope this was helpful for you and if you think of something that should be there is missing or if you feel like contributing, just drop me a line.