Thanks Aaron! Do you make your images and work on them as 16-bit and then save it as CMYK or RGB depending of the journal?

Great. So, let me get your strategy straight.

Then you work your 16-bit photos on ImageJ (as RGB?), then paste (or import?) the photo into Illustrator to build the panels (for Quantification images you add them as eps directly).

The question is, what would be best...to work on your photos as RGB or as CMYK using ImageJ? As you say RGB looks great on the computer monitor which is great for presentation/seminars and so, but if the final destination is printing, would you work with ImageJ on RGB, then convert the photo to CMYK before adding to Illustrator? or work directly in CMYK?

I use almost exclusively linux systems. I have found the following programs useful for the tasks described above; many are available for windows/mac as well:

GIMP (http://www.gimp.org/)

photo/bitmap editing (e.g., photoshop replacement)

Inkscape (http://inkscape.org/)

layout, drawing diagrams, annotating images (e.g., illustrator replacement)

ImageMagick (http://www.imagemagick.org/script/index.php)

very fast command line image conversion, allows scripting

command line conversion tools: epstopdf, ps2pdf (from texlive-extra-utils package)

Note that all of these programs are available for (legal) free download.

Thanks David!

Yes good list from @david i just wanna add adobe ilustrator and coreldraw for vectorial like @aron said earlier. If you use standard office from windows just don't forget when you save image choose for best quality type your image will be better but increase the file size.

@Aaron, great comments above, but I'm curious why you say "The majority of journals use CMYK nowadays". To my mind, the majority of journals used CMYK *historically*, as all journals used CMYK (at some stage) when they existed only in printed form. Nowadays the majority of journals put papers online, and many journals are online-only.

I think it makes more sense for journals to ask for the images as they were created (typically RGB) and then to convert them to CMYK when printing, and leave them as (or convert them to) RGB when putting the article online. What do you think?

Totally agreed!

I agree with David. Inkscape is free and a good choice for vector graphs, gimp for raster.

Personally I use Matlab to make my figures (unless they are microscopy images, in which case I go with photoshop or ImageJ). This way I don't have to remember what little tweaks I did to each figure to get it perfect, everything is written into a code. The same principle applies to R. 

The reason these programs are great is that you can go from raw data, to analysis, to a publication-quality figure in the same software, and in many cases all at once. Matlab allows you to completely customize figures, and exports them to all of the usual file formats (EPS, PDF, TIFF). Furthermore, because the structure of your figures is written in a code (and is therefore just a text file) you can manage the files using version control software and Git Hub so that you never lose any figure formats. 

In the cases where I make modifications to figures, or if I want to make a schematic diagram or a cartoon, I use Illustrator. My impression is that Inkscape is just as good as Illustrator except free, if you can't get Illustrator.

The downside obviously is that both programs have a learning bump to them, and don't make sense if all you want is to get WYSIWYG style point and click figures. In that case, one option is Grapher which is pretty intuitive and produces very nice figures.

http://www.goldensoftware.com/products/grapher

https://inkscape.org/en/)

http://imagej.nih.gov/ij/

Hey Luciano, so how are you preparing your figures now?

Little tip, GraphPad and powerpoint are also useful to prepare your graphs and assemble them... There is sort of an underestimation of powerpoint for making figures but the latest version is very good and enough to sort figures out... (Although you may need to go back to illustrator to change the size of your figures.. but I find PP easiest to assemble...)

Generate figures in MATLAB & export it in EPS format. This is the best quality I have ever got.

Can someone point to a link  to a good tutorial video on making a multi-panel high resolution scientific figure using a software, e.g., inkscape or illustrator?

Photoshop is the best photo editing software and GIMP is the free alternative image editing software

for graph sigmaplot, graphpad also you can copy graph from excel and modify it in inkscape 

Inkscape for 2D and Blender for 3D pictures.

Blender for animations

For instance: https://www.youtube.com/watch?v=RasemoYzsFA

I have recently found a tool called "Daniel’s XL Toolbox" that can be used to export high-resolutions graphics from MS-Excel.

Here is a link for the tool: https://www.xltoolbox.net/

A tutorial to do the exporting: https://www.xltoolbox.net/scientificpublishing.html

Question about EPS format.  Can you view in paint or image viewer or do you need s/w for viewing this format?  When you convert from EPS to other formats do you lose resolution?

Matlab is a good one, another suggestion is Visio, Adobe illustrator, SmartDraw.

hi,

i am using affinity designer and photo to edit both my pictures and figures. it takes some time to get use to it but it is still easier and cheaper than adobe. and now it is available on mac and pc as well.

Sketchup Pro is also very effective .

For graphical figures, either graphpad prism or spss. But graphpad is easier than spss. It is very easy to customize figures like graphs. You can also easily input values and do statistical analysis if you don't know how to use spss. As for tables, Word or Excel is still good enough for me. For graphical abstracts, I'll leave that out on photoshop or sketchup pro. For chemical structures, chemsketch is a good tool.

Very useful tutorials are on the web page of Cornell University and the ORI web page:

http://www.plantpath.cornell.edu/PhotoLab/DigiPhotoTips.htm

http://www.plantpath.cornell.edu/PhotoLab/KnowledgeBase/DigiPhotoTips/BuildingPlates.htm

https://ori.hhs.gov/education/products/RIandImages/guidelines/list.html

https://ori.hhs.gov/education/products/RIandImages/practices/default.html

Fotor...

Try to use Ms Visio

Try Biorender, Its demo looks so cool. Inksapce also good but needs more practice to get expertise.

^^Biorender! (https://biorender.io/)

Has a library of pre-made cells, proteins, membrane shapes, organs, lab equipment, etc. that you can drag-and-drop so you don't have to spend time drawing each element of the figure out yourself. Saves a lot of time for schematic figures...

Origin works great for me with no requirement for coding.

Re "Biorender"... do the pre-designed images make it a touch generic? I find the most fun is making the image (although time cost is high of course). Also, there is a sign up process... is there a counter cost to the sign up? I ask as a colleague said it was good, and emailed the sign up www page out to me and several others.. cant help but wonder if there is an exchange in the background. But Im hoping its good!

You can hardly get a single satisfactory software. The best thing is to you use combine software to achieve best quality. Personally, whenever I draw a graph or picture I export it to corelDraw or adobe illustrator to enhance the quality. You can try that it is very easy.

Try the Origin that is easy to start.

you can try convert the images in TIFF format!!!??

try MS Visio for vector graphics and Photoshop for raster ones

inkscape is very good and descent enough for 2D diagrams and plots! Compatible in almost in all OS: linux, windows and mac.

I think originPro is easy to use

For graphs I used to prefer MATLAB, for graphics CorelDraw and for flow charts Microsoft Visio. As these software are one of the best in their field, thus recommended.

Origin software is user friendly for this purpose.

I usually use matlab/octave scripts for plotting, taking care of the file format of the graph I want to export. JPEG is usually the worse and png is a good compromise. However, pdf, ps, eps, svg, are the best because they maintain the information of the graph which can be changed easily with another program.

For post plotting elaboration I use Inkscape which can handle nicely file format in vectorial form (pdf, ps, eps, svg). I use it also for schematic and I stay as far as possible from power point since it makes it very annoying to export the schematic with the right size, resolution, and format.

I think there is not a single perfect program to use, but there are several habits to avoid especially for newbie students.

Hi,

First of all, taking the photos with a high-quality is important itself from for example microscope or something like that but if we have to do editing on photos I think the Photoshop software is good and sometimes we use Adobe Illustrator software for editing of phylogenetic trees.

I have used MS Visio as it has been suggested by different people here as well. But, the problem comes when you upload the final file of manuscript for journal submission, then, the image get deteriorate (blackish). I have faced this issue earlier. I think it has some problem with compatibility. It has left me to use PowerPoint for image creation. Becuase, I found it comparatively easy to create images than directly in the word.

Started using Inkscape after following this thread. Would surely recommend it. Provides option for exporting at different DPI values, with a host of customizations from arrow shapes to useful labeling alternatives.

Dear Luciano

I use photoshop software most of the time for editing of photos and making photoplate for final

Please see this video

How to Save Excel Graphs as High Quality Images

https://youtu.be/-NwYoayFJbs

You can directly convert plotted excel Plot/Chart from 96 dpi to 300, 600 dpi etc

I've been using Inkscape almost exclusively during the last 4 years.

It's a versatile open-source vector graphics editor (and it's free).

Having vector graphics files allows you to control the quality of the figures, so you can easily adjust and re-use figures from your publications for posters, for example (apart from other obvious advantages of the software).

photoshop and Inkscape

The following app is now my favourite.

https://www.draw.io/

www.draw.io looks really interesting. I just wonder about the future buisness model. Thanks to Orhan Akbulut for the hint.

Photoshop

In person to this, I recommend Microsoft VISIO for creating process flow diagrams, charts and other illustrations.

But in future or in long term application I recommend CorelDraw probable of version more than X2. This software has too much capability and is commercially used by graphic designers.

I would not recommend CorelDraw for beginners. Otherwise you need to spend some time just to learn things around.

Inkscape is more user-friendly and logical software. To start working with vector graphics editors it is a reasonable choice.

All the best,

Anna

Hi,

As different colleagues have said Biorender (biorender.com) is one of my favourites websites to make protocols, schemes or models for your project/paper and It has a lot of images from plants to lab stuffs. Of course, it is useful but until a limit because at specific times could be a little childish or simple for what you could be looking for.

You could see the example attached, every part is free at this page.

BioRender is amazing.

You can use OMERO, its has many good features.

OMERO, BioRender

Adobe photoshop also useful for editing the images and pictures

Use PowerPoint or Paint but save the image or graph with extension (TIFF)

the resolution will be like what seen in the attached file

Definitely BioRender . You can import your own images into it too if you need to include statistical data. It's pretty easy to make figures that are nice and I find it to be much faster than PowerPoint or Google Image Search (which I used before).

GIMP is the best and open sourc.

Adobe Illustrator!!! No doubt, then, you can try also with Inkscape ;-)

InkScape is the best and free alternative to the Illustrator as for me

I recommend having the graphics done by a professional graphic designer instead of buying software. The best tools won’t automatically produce high-end graphics.

Check this: https://www.easyresearcher.com/

Adobe Illustrator is the best software to produce images that don't pixelate. It is easy to learn and the graphical interface is very easy. Try adobe illustrator.

Dear researchers, which's the best software for biology?

Dear Luciano:

As many scholars states above, Adobe Illustrator is one of the most used, and indeed is "the most used" by renowned journals such Nature. I attach a file that you could download, affirming AI file format are the first in the list of acceptable one in this prestigious journal.

Hope this could help you

Samir Berkat Use chemdraw for all biology and chemistry related graphics, You can also use Biorender, Inkscape.

Avinash Kumar thanks so much Sir for the reply.

For diagram representing models, concepts ore mindmapping in Humanities, I use "yED", free and easily usable.

Latex might by a good tool for documentation.

This is a really good question and really, it depends on what your trying to wrangle. For confocal images, i much prefer imageJ and then illustrator (there are some really good free tutorials out there to learn the basics of this software). I do save in TIFF format, never in jpeg as you lose the quality upon resizing. I do like chemdraw when wanting to illustrate chemical structures. for statistical analyses, making tables and graphing data, i do like matlab. Its pretty powerful once you learn how to use it properly, especially livescript as you can setup, test, then execute a protocol for streamlining or to simplify repetitive tasks.

Late answer, but:

I find PowerPoint is actually incredibly user-friendly when it comes to making graphics. I have shared this technique with many colleagues who have no 'artistic' background, and they have created incredible images as well!

Here is a brief guide that I wrote for generating graphics in PPT, using an insect as an example: Method A brief guide to PowerPoint graphics

Cheers

ImageJ

Check this: https://www.easyresearcher.com/

I also have the exact same question. My problem is quality loss of the final figure when putting several images/graphs etc together to present as one figure. Any thoughts on this?

Inkscape is really easy to use (also free) especially when one wants to conjoin multiple plots and label them.

Eirini Evangelia Thomloudi This tutorial video in youtube may solve the issue

https://www.youtube.com/watch?v=TEFJBeZmsCI

ImageJ is useful for microscopic image analysis like FFT and others

I would say Biorender is the best app to make graphical abstracts or figures for publications https://biorender.com/?rg. I still ‘assemble’ my final figures in Adobe Illustrator but my colleagues who don't want to learn Adobe do their final work in biorender with no issues

Amos sotware

Paint, Photoshop, ChemDraw, Origin 2020, Matlab, PowerPoint, Excel Graphs, biorender, CorelDraw, Inkscape, Mind the Graph etc.

https://biorender.com/

ggplot - https://rstudio.com/wp-content/uploads/2015/03/ggplot2-cheatsheet.pdf

Matplotlib - https://matplotlib.org/

Seaborn - https://seaborn.pydata.org/

Bokeh - https://docs.bokeh.org/en/latest/index.html

pygal - http://www.pygal.org/en/stable/

Plotly - https://plotly.com/

geoplotlib - https://github.com/andrea-cuttone/geoplotlib

D3.js - https://d3js.org/

Pandas Visualization - https://pandas.pydata.org/pandas-docs/stable/user_guide/visualization.html

Altair - https://altair-viz.github.io/

Adobe Illustrator - https://www.adobe.com/ie/products/illustrator.html

CorelDraw - https://www.coreldraw.com/

Inkscape - https://inkscape.org/

OriginPro - https://www.originlab.com/origin

GIMP - https://www.gimp.org/

gnuplot - http://www.gnuplot.info/

Draw.io - http://draw.io

Google draw - https://docs.google.com/drawings

ConceptDraw - https://www.conceptdraw.com/products/drawing-tool

Frida Gorreja unfortunately, you cannot remove the watermark in the free version.

Hi there,

No matter which program you will use to create the figures (maps, graphs, etc.), the best way to keep the quality is to export the figure as an .eps file and to continue editing it in another (e.g. Illustrator, Photoshop) software. When exporting .eps, you keep the information in vector file, not raster, which is the most important if you want to produce high quality figures.