Essential Computer Graphics Techniques for Modeling, Animating, and Rendering Biomolecules and Cells

A Guide for the Scientist and Artist

Giorgio Luciano

• Publisher: A K Peters/CRC Press
• Year: 2019
• ISBN:
  9780429624117
• Edition: 1
• Topic: Informatica
• Subtopic: Grafica per computer

The book helps readers develop fundamental skills in the field of biomedical illustrations with a training approach based on step-by-step tutorials with a practical approach. Medical/scientific illustration mainly belongs to professionals in the art field or scientists trying to create artistic visualization. There is not a merging between the two, even if the demand is high. This leads to accurate scientific images with no appeal (or trivial mistakes), or appealing images with huge scientific mistakes. This gives the fundamentals to the scientist so they can apply CG techniques that give a more scientific approach creating mistake-free images.

Key Features

• This book provides a reference where none exist.
• Without overwhelming the reader with software details it teaches basic principles to give readers to fundamentals to create.
• Demonstrates professional artistic tools used by scientists to create better images for their work.
• Coverage of lighting and rendering geared specifically for scientific work that is toturoal based with a practical approach.
• Included are chapter tutorials, key terms and end of chapter references for Art and Scientific References for each chapter.

CHAPTER 1

Preface

During 2013, while I was forum leader for the lighting challenge at the CGtalk forum, Kirsty Parkin was looking for ideas for new workshops/courses at the CGSociety. I read her message while I was at work at the National Research Council, and then the cover of a scientific journal got my attention. It was a very high impact journal devoted to a wide range of scientific disciplines. Although the concept on the cover was clear and sound, the 3D graphics looked cliché and dated, so I sent an email to Kristin with this subject: “What do you think about creating a workshop about scientific visualization?” My aim, at that time, was not too ambitious. I would have been very happy just to be able to teach the basics of 3D to researchers, since I had already taught computer graphics courses for my colleagues, and I was very satisfied with the results of just a few days of teaching. It was very funny to open a small world for the scientists involved, letting them know the basic concepts of 3D modeling and shading and seeing how they enjoyed creating their first image (the mandatory teapot with a shader applied) and a basic three lighting setup in all its glory! It was also a way to exchange scientific ideas with other people; it was enriching to understand their approach to this subject after the more artistic approach to which I was accustomed from moderating threads and giving feedback at CGTalk.

Kirsty thought that the idea of teaching a course in biochemical visualization (actually, we were quite unsure what to call the workshop) was interesting since it was a field that was growing, testified by the fact that they had already created a CGChallenge about the visualization of the HIV virus. She was interested in the subject, but it was not easy to find people versed in both science and CG. So, thanks to Kirsty, I started teaching the first Biomedical Illustration Workshop at the CGSociety. I admit that I was very anxious and happy at the same time since I was not sure what to expect.

The first challenge I had to face was a big dichotomy among my students. Half of them were scientists with almost no experience in 3D; the other half was made up of professionals working in the CG industry (mainly motion graphics and advertising) who wanted to know what skills were needed to create their illustrations (still images, small animations, previz, movies, etc.).

I went for a customized approach for each student, trying to focus on his or her strong and weak points, suggesting where and how to improve with the help of correct references and exercises of increasing difficulty.

I soon realized that, even if the tools evolved quickly, the work of an illustrator is to create bridges between scientists and an audience in an effort to represent concepts as accurate, plausible, and at the same time as beautiful and artistic as possible. The caveat is what every translator faces in his or her work. In Italy, my country, there is a phrase traduttore traditore, translated literally as translator traitor. In the effort to represent concepts in an artistic way and to make them approachable for a wider audience, we should never forget the rigor of what we are depicting. This book represents a small effort to help illustrators learn new tools and scientists become better acquainted with the basic concepts of illustration.

Science has made giant steps in the last years toward making available data on the structure of molecules, cells, human and animal anatomy, etc. Often, the beauty of reality oversteps our artistic vision. The more information and tools we have on the concepts we are going to illustrate, the better. In this book, I will give information on where to find it and tools that can be helpful while representing scientific concepts.

Knowing the basics of 3D software will also improve the way we understand concepts and create mental models since it will force us to have a clear vision of what we want to communicate to the world.

For Whom Is This Book Intended?

1. Scientists and researchers that would like to understand the basics of animation/lighting and rendering in 3D graphics
2. Artists who would like to know more about the scientific software used in the biochemical/medical field
3. Students of CG who would like to know more about biochemistry/biomedical rendering/animation and to look at the software used in the biomedical field
4. Teachers who would like to represent in a catchy way the concepts of the biochemical/medical field and want to learn the basics of illustration software

Special attention will be dedicated to the Edutainment world. The main effort of the book is to merge the use of scientific software and mainstream 3D packages in a workflow to produce artistic and pleasant images with strong scientific roots. If you are a 2D/3D artist, this is NOT a book for becoming a scientist in the biomedical/biomolecular field, even though it will show you fascinating concepts and ideas in these fields. It is, rather, a starting point for gathering references for creating your own path toward working with scientists to create a common background.

Style of the Book

The book is informal, despite my best effort to be rigorous while describing scientific concepts. I wrote every chapter to be self-sufficient and to encourage the reader to explore his or her own topic of choice and create a personalized learning path. For this reason, I preferred to include a selected list of references at the end of each chapter. I listed only what I think are the indispensable and mandatory references in order not to overwhelm the reader, considering the increasing quantity of available literature on each topic

Most chapters include

• Keywords
• A chapter outline
• Focused sessions on specific topics that describe special skills and tools for achieving a specific rendition of the concepts presented
• Tutorials on the key illustrations presented in each chapter
• Exercises to help the reader build his or her knowledge on the subject
• Icons of the software used to create specific tutorials and images in order to help the reader choose those most appropriate

Which Software?

I started to “play” with 3D software in the ’90s when I was a college student. The first program I used was Autodesk 3D Studio Max. I like to learn new skills, so during the years I’ve tried Maya, Cinema4D, and Pixologic Zbrush; I’ve also started digging into Modo and Houdini (hard to learn but unrivaled in the field of generative and procedural modeling). Now Zbrush, Cinema4D, and Modo are indispensable tools of my everyday job.

I have tried Blender, and I’m very happy that I did. It is a pro tool with tons of add-ons and is Python scriptable. Since I have to use Python quite often to manipulate my data, I feel at home and use it to create examples of scripts for procedural modeling.

When I teach at Computer Graphics Master Academy (CGMA), every student has a different background in 3D and is skilled in specific software. The first question everyone generally asks is: May I attend your course if I use Software X? The second most asked question is: Is Software X better for biomedical illustration than Software Y? Is there a software that has all the features we need?

The answer is: “Of course not, otherwise we all would use THAT software.” Everyone has personal preferences and different pockets. It would be a huge task to show how to create illustrations with EVERY 3D software, and it can be self-limiting to try to accomplish everything with just ONE software. In this book, I will focus on the similarities among software I use, and I will teach the general concepts behind all of them. In this way, you will be more flexible and it will not be too complicated to shift the tools for your work depending on the preference of the studio where you work or the development of new software.

When we work on biochemical/biomedical medical representation, we will need to use a lot of very specific packages used in everyday work by scientists. Luckily, a lot of software in the technical field is open source, free, and available for several operating systems.

In the (rare) case that there is a task that can only be accomplished with one specific software, I will highlight it.

My Workflow

This section relates to the process of creating a product for a wide audience, not a product for peers. I start almost every project with paper and pencil. I write down a few lines and create a very primitive storyboard of how the animation should look. In this stage, I prefer pen and paper to software, since it gives me total freedom to doodle. Since it is a kind of “creative” project, I need to feel free. The second stage is about modeling. First, I try to find as many references as possible. If the animation is about organic molecules/nanomachineries, I look at the protein data bank (PDB) and eventually download the files needed. Then I search the EMDB database to see if there are other data available with techniques not present on the PDB site. After this step, it is time to import the coordinates of the molecules into the dedicated software: Chimera and VMD. I look at the molecules, check for a suitable representation among the several available, and eventually create a small animation. Then I export the animated model into a format that can be imported in my main 3D application (generally alembic format abc or dae).

If I need to represent inorganic complexes and molecules, I also use Vesta and Nanoengineer Nanorex, dedicated to this branch of chemistry.

I refine the model in Zbrush and export it in order to use it in Cinema4D, Modo, and/or Houdini. Cinema4D is quite an easy software, and I prefer it for easy rendering, Modo is my battle horse, since it can do almost anything. Houdini is my companion for special effects and animation (it can be used for modular modeling, as we will see later in the book). I set up lightning and then shaders (textures and the properties of the molecules/objects represented) with the help of specific software such as Substance Designer. Then I animate the models, give a fast try at rendering using low settings, and then start again and set up the details in the scene. After the animation is ready, I render all the frames and export them in an uncompressed image file (TIF or TGA). My favorite render engines are Arnold, Renderman, and Mantra. I composite my passes using Blackmagic Fusion, Nuke, or Natron.

A few key points:

• Put the ideas on paper using traditional techniques or very easy tools so as not to focus on the tools (pencil and paper or a quick sketching application)
• Search for references: Probably the most important part of the whole process. Never get tired of doing it; every minute you spend searching reference will be well spent.
• Create/Import your model.
• Create mockup animation if needed.
• Light your scene.
• Apply shaders and texture (the appearance of your model), and recheck your lighting.
• Render the animation (low resolution to check if everything is in place).
• Recheck everything and repeat the necessary steps.

Advice about File Naming and Organizing Your Files

KEEP YOUR FILES CLEAN! (uppercase for emphasis intended). Keeping your files organized is one good habit that will save you tons of time, in comparison to keeping everything in unique folders with names like untitled01.3ds, first.ob, 01, second.obj, final_one.bck, really_final_one.fbx etc.

Even if it seems obvious and quite easy to do, its complexity can escalate quickly depending on the size of your project. A very good, generic introduction that will help you keep your non-CG files in a clean and organized structure is included in the book, Guerrilla Analytics: A Practical Approach to Working with Data. If your everyday job includes using a computer (so every job), I strongly encourage you to read it. It is really worth your time. After reading several threads on this topic on different pro forums (CGSociety, Polycount, etc.), and with the help of Hilaire Gagne (an animation pro), I choose to organize my files using this tree

 –Assets –Lighting Test –Models –fbx –obj –abc –References –Shaders –Textures –non pbr –pbr 

In this way, you should have everything at hand and find it quite quickly.

Since the chaotic me sometimes needs to take a pause from the company of the OCD me, I created a folder called daily_box. The rule is that I can put everything I want there, but at the end of the day, I MUST clean it out.

Remember that every studio has its own very strict convention for naming. This is not only because of OCDs but also because scripts need to find the files with their own exact names.

The convention I prefer to use is to put underscores (since not all OSs like spaces) and a small description of the file, for example

 Body3D_anatomy_v1_remeshed BloodCells_vein_animation_v1_no_texture 

If you succeed in sticking to it, this will greatly help in your everyday work. If not, there is always the UNSORTED folder as a last resort.

Software and Hardware

Every scene presented in the book was tested with the following configuration.

Software: Modo 10.2v4, Cinema4D R18, Houdini 16.0.2.54, Arnold Render 4.2, Substance Designer 6.0, Substance Painter 2.5. Chimera 1.01, Vmd...