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What is your workflow for generating figures for publications/posters?
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DGChaos Offline
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Post: #1
What is your workflow for generating figures for publications/posters?
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Mine's pretty simple and straightforward: Generate all figures in MATLAB (or on rare occasions, Python) and export as .emf/PDF! I may add some figure labels or annotations by hand using Inkscape/Powepoint after MATLAB has finished generating the raw figures.

And then Overleaf/LaTeX to write up results or Inkscape/Powerpoint to make a poster.

Just curious about what everyone else is doing. In case y'all have hacks and tricks I like, I may incorporate them into my workflow. Smile

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PhD Student in Biomathematics, Computational Biology, and Bioinformatics at Duke University

I won't recommend or rank universities for you. However, if you need specific information about PhD programs in the biomedical sciences, tag me, and I'll try to help.
04-28-2017 06:36 AM
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Post: #2
RE: What is your workflow for generating figures for publications/posters?
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My workflow is same as yours.

MATLAB is pretty terrible in making plots and graphs (Python is better, R is even better). I have to stick to MATLAB though especially for creating custom results for image analysis (I work in computer vision). Sometimes reviewers want to see results made with the published MATLAB codes of other authors, and since MATLAB is the lingua franca of computer vision, I often end up using it for generating figures. But if I have option I stay away from MATLAB.

I save the figure in .eps format (to include in LaTeX) if further annotation is not required. Otherwise, I open it in MS-Powerpoint, do the needful annotation, and use Adobe Photoshop to save it in .eps format. If I need to incorporate mathematical expressions inside the figure (which I often need), I use a nifty powerpoint plugin called IguanaTex. As a side note, if you use MS-PowerPoint for preparing talks and you wish you could use beamer like features to write maths expressions inside PowerPoint slides, try IguanaTex!

That being said about conference/journal publications, I must mention that web publishing has better and faster options. For example, you can publish the whole MATLAB script (MATLAB supports LaTeX scripts) for web publishing. However, I mostly use iPython Jupyter Notebook for that purpose (I am an avid fan of iPython Jupyter). I know I might have deviated a bit from your question on LaTeX/PDF related workflow, but looking at the trend, I won't be surprised if web publishing becomes the norm in five years down the line. We shall not be writing papers, we would be writing blogs then Very Happy

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04-28-2017 05:54 PM
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Post: #3
RE: What is your workflow for generating figures for publications/posters?
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Is LaTeX still alive?

MATLAB is the standard in my Lab.

Good to know about IguanaTeX.

Cheers

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04-28-2017 07:44 PM
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RE: What is your workflow for generating figures for publications/posters?
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In Materials Science, Python is one way ofcourse. A more commonly used method for figures, especially for generating spectra from different spectroscopy methods, would be Igor Pro or Origin. Once can save thefigues as .jpeg and then edit on Inkscape or PowerPoint.

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05-07-2017 01:36 AM
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Post: #5
RE: What is your workflow for generating figures for publications/posters?
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ggplot in python / ggplot2 in R. Powerpoint for those darned system architecture plots.
05-11-2017 04:56 AM
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DGChaos Offline
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RE: What is your workflow for generating figures for publications/posters?
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(04-28-2017 05:54 PM)Gaussian Wrote:  My workflow is same as yours.

MATLAB is pretty terrible in making plots and graphs (Python is better, R is even better).

Are there specific things that make plotting on Python (or R) better than MATLAB. I actually use both Python and MATLAB for plotting my data (mostly line/dot plots, surface plots, and heat maps), but recently gravitated toward MATLAB just because I found it easier to make aesthetically pleasing (multi-panel) plots. But if there's something significantly better about Python or R for plotting that I am missing out on, I will make the switch! Smile

(04-28-2017 05:54 PM)Gaussian Wrote:  I use a nifty powerpoint plugin called IguanaTex.

This is awesome! I usually use MATLAB's TeX compiler to generate equations alongside graphs, and then copy it onto my slides, but being able to do the same directly on PowerPoint would be awesome!

(04-28-2017 05:54 PM)Gaussian Wrote:  That being said about conference/journal publications, I must mention that web publishing has better and faster options. For example, you can publish the whole MATLAB script (MATLAB supports LaTeX scripts) for web publishing. However, I mostly use iPython Jupyter Notebook for that purpose (I am an avid fan of iPython Jupyter). I know I might have deviated a bit from your question on LaTeX/PDF related workflow, but looking at the trend, I won't be surprised if web publishing becomes the norm in five years down the line. We shall not be writing papers, we would be writing blogs then Very Happy

Very interesting point!

(05-11-2017 04:56 AM)sinx_123 Wrote:  Powerpoint for those darned system architecture plots.

Ha ha ha! I wish there was a LaTeX-like thing for flowcharts and stuff. It probably won't be pretty, but I hate formatting stuff of that nature.

EDIT: Googled this and learned about Tikz. I will give this a whirl (I should have searched for this earlier! Grawr.): https://www.sharelatex.com/blog/2013/08/...s-pt3.html

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PhD Student in Biomathematics, Computational Biology, and Bioinformatics at Duke University

I won't recommend or rank universities for you. However, if you need specific information about PhD programs in the biomedical sciences, tag me, and I'll try to help.
(This post was last modified: 05-14-2017 12:49 AM by DGChaos.)
05-14-2017 12:42 AM
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RE: What is your workflow for generating figures for publications/posters?
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(05-14-2017 12:42 AM)DGChaos Wrote:  Are there specific things that make plotting on Python (or R) better than MATLAB. I actually use both Python and MATLAB for plotting my data (mostly line/dot plots, surface plots, and heat maps), but recently gravitated toward MATLAB just because I found it easier to make aesthetically pleasing (multi-panel) plots. But if there's something significantly better about Python or R for plotting that I am missing out on, I will make the switch! Smile

I am particularly frustrated by the white boundary (which you can not control) that MATLAB keeps around each figure. Displaying images in their true size used to be a problem in older version. Varying colormaps in different subplots inside the same figure window used to be an issue too. In fact, MATLAB's colormap package is so bad: the discretization artifact is terrible. Also, MATLAB is painstakingly slow in making 3D visualization (VTK and Mahotas work like charm)! The python, especially R, have way more plotting options (I still don't know how to show "intervals" in MATLAB plots). Moreover, they look more elegant too.

Many of those limitations might not exist with the current versions. However, I am no longer associated with academia, and since commercial MATLAB licenses are supremely expensive I don't have the opportunity to stay up to date with each and every MATLAB release (a strong reason to befriend open source). Also, my comment is heavily biased toward computer vision. You may not need to pay attention to all such details if your domain is different Smile

Since domain has come into discussion I have a question for you if you do not mind. I see you work in cell biology. Do you use microscopic image analysis for your research? I would be interested to hear your experience, or perspective on present trends, if you have any such relevant exposure. What I want to know is, what image analysis has in offer for systems biology? Smile

Gaussian

There was an old man of Esser,
Whose knowledge grew lesser and lesser,
It grew at last so small -
He knew nothing at all,
And now he calls himself a researcher!


I do not evaluate MS profiles
(This post was last modified: 05-16-2017 10:10 AM by Gaussian.)
05-16-2017 10:07 AM
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DGChaos Offline
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Post: #8
RE: What is your workflow for generating figures for publications/posters?
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(05-16-2017 10:07 AM)Gaussian Wrote:  I am particularly frustrated by the white boundary (which you can not control) that MATLAB keeps around each figure. Displaying images in their true size used to be a problem in older version. Varying colormaps in different subplots inside the same figure window used to be an issue too. In fact, MATLAB's colormap package is so bad: the discretization artifact is terrible. Also, MATLAB is painstakingly slow in making 3D visualization (VTK and Mahotas work like charm)! The python, especially R, have way more plotting options (I still don't know how to show "intervals" in MATLAB plots). Moreover, they look more elegant too.

White boundary! Always detested it. I use the tight_subplot (for those interested) function to eliminate white boundary, but aye, Python's plotting functions look more flexible. I have a lot of additional code that goes into making my MATLAB plots look pretty, so maybe it is time I gave Python another shot ha ha.

(05-16-2017 10:07 AM)Gaussian Wrote:  Since domain has come into discussion I have a question for you if you do not mind. I see you work in cell biology. Do you use microscopic image analysis for your research? I would be interested to hear your experience, or perspective on present trends, if you have any such relevant exposure. What I want to know is, what image analysis has in offer for systems biology? Smile

Sure! Happy to answer that.

I do use microscopic image analysis in my work. Occasionally, I will write up simple tools for analyses in MATLAB, but if that starts to take too long or my analysis calls for some kind of GUI, I use Fiji. For tracking fluorescent stuff that moves around, I use Volocity and I typically deconvolve crappy images with Huygens. These tools seem pretty popular with other students too, so I'd assume they are kind of industry standard.

More specifically, the work I do typically involves looking at how some proteins move around inside a cell and comparing those movements with a partial differential equation model. The way to look at the protein is to attach another fluorescent protein to it--this then allows one to see aggregates of the protein under a microscope. Most of the analysis I do is not complicated (threshholding, finding CV in a region of interest, simpler tracking algorithms) or fairly standardized (like image stabilization, deconvolution). But one thing I (and a lot of biologists) wish I had is software that is good at recognizing cell shapes and segmenting them automatically. Fiji has a lot of good segmentation algorithms, but they don't always work. I tried my hand at building tools for myself, but quickly realized that it is a whole area of research by itself and was taking away time from my PhD work, so i gave up ha ha. I hope this answers your question! Smile

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PhD Student in Biomathematics, Computational Biology, and Bioinformatics at Duke University

I won't recommend or rank universities for you. However, if you need specific information about PhD programs in the biomedical sciences, tag me, and I'll try to help.
(This post was last modified: 05-17-2017 10:32 PM by DGChaos.)
05-17-2017 10:30 PM
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RE: What is your workflow for generating figures for publications/posters?
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DGChaos
Good to know the valuable information! Thank you for taking time to answer my question. I appreciate your prompt response.

Can we take this discussion offline if you don't mind? I have some interest in this area which can not be shared in a public setting.

Gaussian

There was an old man of Esser,
Whose knowledge grew lesser and lesser,
It grew at last so small -
He knew nothing at all,
And now he calls himself a researcher!


I do not evaluate MS profiles
05-17-2017 10:40 PM
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DGChaos Offline
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RE: What is your workflow for generating figures for publications/posters?
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(05-17-2017 10:40 PM)Gaussian Wrote:  @[DGChaos]
Good to know the valuable information! Thank you for taking time to answer my question. I appreciate your prompt response.

Can we take this discussion offline if you don't mind? I have some interest in this area which can not be shared in a public setting.

Sure, pmed you!

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I won't recommend or rank universities for you. However, if you need specific information about PhD programs in the biomedical sciences, tag me, and I'll try to help.
05-17-2017 10:49 PM
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