First Neuron Animation Sequence Update

Updated version of the neuron dendrite growth animation that I'm working on.

-Work In Progress-

Synapse Animation Sequence

Work In Progress BioMations.com Synapse Animation Sequence

Maya Adobe Primiere Pro Blogspot.com

Neuron Growth Practice - Take 2

Continuing to refine animation of the neuron growth and connecting sequence.

Animated Neuron Growth Practice

Fun with blend shapes and animation keys.
*Work in progress*

New Project: Short Neuron Animation

I'm currently working on a Neurological animation to give myself a temporary visual break from my CF Animation.

SIGGRAPH Convention and Conference Postcard Announcement

SIGGRAPH Convention and Conference Postcard Announcement
3 -7 August Siggraph Computer Graphics Convention
Poster Exhibitor

Siggraph Presentation!

(Sorry for the lack of updates, I've been in Turkey for the past two weeks.)

I'll be presenting my poster about the CF Medical Animation at the 2009 Siggraph Computer Graphics and Animation Convention in New Orleans in early August!

Website Count!

Thank you for all the great responses and sharing my website with others. This past Wednesday and Thursday, I had over 200 hits on my website from almost every state in the US and from other countries such as Australia and Canada.

Thank you all, and please, send me your feedback! I would love to further touch up the animation and will do so for the next few months.

Is there another cause you would me to create an educational animation for, please contact me! I'm open to ideas.

info.biomations@gmail.com

My Final Thesis Animation

This is my Final Thesis Animation for the Short.
It will continually be a work in progress.
To view at a better resolution, please visit my site at www.BioMations.com.
Enjoy! Feedback is always welcome!

Siggraph Late-Breaking Timeline

I have updated my application and submitted my materials for the Siggraph Late-Breaking Poster Submissions. I will be notified of the status of my application between the 24th and 25th of May.

This year's SIGGRAPH 2009 Convention will be held in New Orleans from the 3-7th of August.

Final Thesis CF Med Animation posted www.BioMations.com!

Please visit my web page at www.BioMations.com to view the full cystic fibrosis medical animation!

Rendering!

My thesis project is due this Saturday by 9am. I need to have everything complied by Thursday evening, just as a precaution. Currently I am rendering my final autosomes.

My 8-page 11 font, 1" margins, thesis paper was due yesterday.

My postcards for the thesis exhibit have finally arrived in the mail today, and I will deliver them to school tomorrow.

After this deadline, I will aim to resubmit my poster submission to Siggraph late-breaking deadline of May 6th.

Mucus!

Faking mucus without RealFlow Dynamics. I'm currently rendering out 200 frames with an estimated render time of 30 hours.

CFTR - Na+ Build Up

Na+ build up around the closed gated channel of the CFTR cell membrane. (The blue squares are the Na+ molecules.) Now that all the modeling, light texturing, lighting, and animation has been completed, I am ready to start batch rendering out the frames. While those frames batch render, I'm going to fix up the texture on the lungs.

CFTR Cell Camera 2 Rendered Shot

Currently finished with the CFTR cell itself. The red blob is the protein that connects with the CFTR to close the gated channel (the largest object) on the surface of the cell membrane. When the gated channel closes, the cell no longer accepts or releases Na+.

CFTR Cell Model Rigged

I rigged the CFTR Cell Model so that I could animate the cap open and closing.

Rigging Fun- CFTR Cell

CFTR Cell Block Model Progress

Block model is almost done. Next step, texturing, rigging, and lighting. The texture for this sequence will be very flat and have more of a 2d illustrated look to it.

CFTR Cell Block Model Started

Block model for the CFTR cell. Work in progress! Hoping to complete this model from start to end by tonight.

Lungs & Trachea Shader Tests

I'm not much of an organic modeler, but I've completed the lung and trachea models for the medical animation. Here is an image of the shader and texture test that I'm now running. I'm hoping to have this scene animated and rendered by in a few hours.

Red Blood Cells!

Work in progress..

Cells!

Work in progress..

Siggraph Poster

Although my poster submission into the 2009 Siggraph Animation convention was denied today, I received some really great feedback from the review board. I am very thankful for the review comments, and will definitely learn from my mistakes!

My new goal is to resubmit my poster application for the late breaking deadline, which is Wednesday, 6 May 2009. This will come just days after my animation will be completed for my senior thesis gallery showing on the 4th of May.

A few excerpts from my poster review from Siggraph:

1. To have "included an animation" of the work in progress. This 2nd around, I will make sure that I have a movie file included.

2. "An animation like this could potentially be useful as an educational tool. However, the abstract does not describe in detail how the animation was created." This was my mistake. For my next abstract writing, I will make sure that I go into more detail and without grammatical errors.

3. "In general, I think the submission is good, relevant, and interesting to many." This is the most inspirational feedback! Thank you!

4. I also need to address why I used the tools that I did, and why I chose to approach the animation in a realistic way. I will make sure to do this next time!

5. More samples. This should be easy to fix, as I will now have 90% of it completed.

Again, I am really thankful for the feedback.

~I'm Living and Learning :)

Lung Block Model Progress

In the midst of modeling out the lungs. Should be finished texturing and modeling out the trachea tomorrow.

Photoshop Effects: My Chromosome Image

Here's a Photoshopped version of my chromosome image that I rendered yesterday. One of my friends had suggested that I use the burn tool in Photoshop. The result was this:

I then got carried away and created a darker image. I like the effect the darker image has on the chromosomes. I'll go back into Maya and try to create darker, and more stunning chromosomes based on this image.

Maya Texture Ramps

After a few hours in the labs, I finally gave up on the x-ray shaders in Mental Ray and used Maya texture ramp nodes. I've finally rendered out a decent image that I'm happy with for the chromosomes. I'm going to go eat something now... I haven't even had lunch yet and it's almost 4pm!

How to texture chromosomes?

I've just ompleted the block models of the chromosomes. Now I'm trying to figure out how to texture them! Here's a test render. I'll be taking the models into zBrush tonight to add more modeling detail.

Lungs- 3d Block Model Started

Screen Capture of the 3d Lungs Block Model Started:

(3d model is in the middle and multi-coloured)

CFTR Cell Block Model Started

Screen Capture of the CFTR Cell- 3d Block Model Started:

Stylized dna strand

Today's finished product. I am now batch rendering for a movie file.

dna block model with Mental Ray shader

Test render of the dna strand model with a dgs_material shader. The render is very blown out, but it's just a test render. Next step: refining the model and reducing the faceted/chucky look to the strands.

dna Modeling in NURBS

I found a really great way to easily model a dna strand with NURBS, by using nurbs circles and surfaces. Here are just a few screen caps of my process.

Fatter Cilia (Still Image Render)

As suggested by my father, the cilia in the previous cilia/mucus river needed to be much thicker. Here is a new still image render of the cilia in the mucus river. Much better!

*Click on the image to enlarge for more detail.

For This Week's Agenda:

1. My faculty mentor, Mr. Baker, has told me about the new nParticles demonstration for Maya 2009. This week I will be doing R&D with nCloth dynamics and nParticles for creating mucus and other particle matter for the short.

2. Completing the block and rough models of mucus river with actual strands (nurbs geo) of cilia for a fly though shot.

3. Storyboard illustrations will be posted.

4. Complete first sequence models: chromosome, Punnett Square, title blocks.

5. Launch www.BioMations.com website. Home to Phoebe Coleman's online 3d digital animation and photography portfolio. | copyright 2009 www.BioMations.com | Complete with demo reel for application to LucusFilm Internship.

Extended Poster Description PDF completed

I completed my application for poster submission to the Siggraph conference a few minutes ago. The poster description in pdf format is complete! Here is an image of the one-page extended description of my work in progress. And although my poster application may not make the cut, it was good for me to get all of the paperwork together in a cohessive unit.

I will be notified of my rejection or acceptance by 21 April 2009.

Test Render 01 Abstract Image

Here is a test render for the abstract image that I will be turning in for the poster submission for Siggraph 2009.

FEb 18- Siggraph Poster Deadline

Currently, I am working hard to meet the Feb 18th Siggraph 2009, General Submission Poster Deadline.

Items needed: Abstract in pdf form:

1-page extended description and summary of my work in progress.

Item needed: Representative image in jpg form:

"At a minimum, submissions require one clear digital image of the highest print quality possible, pixel resolution of at least 1500 x 1200 (at least 300 dpi at 5 inches wide, with depth proportional) or the highest possible screen grab. Images must be submitted in a 24-bit (RGB, 8-bits per channel) uncompressed, highest-detail JPEG format file possible. A standard ICC color profile of sRGB is also recommended and will be assumed if not specified. Avoid embedded rules, layers, tags, masks, color models (for example, CMYK), etc. If in doubt, use an image editor to paste into a new file."
Source Link: http://siggraph.org/s2009/submissions/representative_images/index.php

Exciting Update! News from the CFF Colorado Chapter!

Copyright permission granted!!! Received this this morning (edited for website blog):

"This sounds like a very cool project! You are more than welcome to use any wording on the website that you would like to.... I would love to see it upon completion (or at an earlier phase if I can help) and I think it could be a very useful tool for us to use when speaking to donors, sponsors, event participants, volunteers, etc. It's also something we may be able to link to on our website. I have attached our logo in case the one you're finding on the website isn't great quality - let me know if there's anything else you need. Keep me posted on your progress!"

So very cool!

Mental Ray and other logistics...

Here are some format logistics:

Render Engine: Mental Ray
Render Image Size: HD 1080 (1920x1080)
Lighting: HDRI and others (point, spot, and directional)
Surface Models: Nurbs to Polys and Polys
Compositor Software: Adobe Premiere Pro and After Effects
Audio: music and narrative dialog*


*Narrative dialog and exact script are awaiting pending copyright permissions.

Block Model 01

(I will post storyboards up after this weekend... Need to hook up my scanner at home.)

Here are examples of the block modeling process. Block models are used to as placement holders while modeling.

Cystic Fibrosis Transmembrane conductane Regulator

Here is an image of the CFTR Channel at an open stage. In the image to the right, taken from an online source (http://old.schoolscience.co.uk/content/5/biology/mrc/3/page3.html), is a cross section of an epithelial cell membrane.

Bill's description of the CF gene for the CFTR image:

"The CF gene codes for the Cystic Fibrosis Transmembrane conductance Regulator or CFTR for short. The CFTR is found on smooth tissue throughout the body, most importantly in the airways and the pancreas. The CFTR is an ion channel that helps move water into the mucus in the lungs making it less viscous and easier to clear from the airways. While there are numerous mutations in the CF gene they all lead to a dysfunctional CFTR that is inable to pump ions across the membrane onto the surface of the lungs. This dysfunctional ion channel (CFTR) leads to mucus that is too thick for the cilia to move out of the lungsand the mucus builds up."

Here is an example of the CF punnet square. Since CF is a double recessive genetic trait, only those who land in the lower right-hand corner box will have CF. The top right and lower left boxes indicate those who are carries of CF.


Image source: http://www.youtube.com/watch?v=l0dDhKFk2HU&feature=channel_page

Dates & Goals

January 2009: Start preproduction and complete storyboards, script, and all other pre-visualization aspects.

January 23, 2009: Start animation research

January 29, 2009: Finish rough script

Feb 1, 2009: Complete dance animation for College of Arts & Media Student Orientation Presentation

February 1, 2009: Apply for UCLA, MFA program

February 1, 2009: Apply for Roski School of Fine Arts, MFA program

February 1, 2009: Create template for poster to submit. Set up demo reel website for Lucas Film Masters Program and Summer Internship Application.

February 6, 2009: Complete storyboards for medical animation. Create a list of all models needed.

February 9, 2009: Finish list of all models need. Commence modeling of all objects needed for the animation. Start texturing, lighting, and rendering of key boards to put together for the Feb 18^th poster deadline.

February 6, 2009: El Pomar Leadership Summit- Weekend off from production for leadership conference

February 15, 2009: Apply for SCAD graduate program

February 18th, 2009: Poster of a work in progress animation submitted to Siggraph 2009 Student Poster competition

February 19, 2009: Send clips of animation and copy of the poster to faculty mentor and doctors at the Cystic Fibrosis Foundation for feedback.

February 19, 2009: Put together demo reel and application for Summer Internship.

February 28, 2009: Apply for LucasFilm Jedi Academy Summer Internship

March 2nd: 80% of the productions complete to submit the animation to the SIGGRAPH 2009 Student Competition

March 6th, 2009: Send 2nd round of clips of animation to faculty mentor and doctors at the Cystic Fibrosis Foundation for feedback.

April 24th, 2009: Finish render and start composting and post-production process.

May 6th, 2009: Optional- Poster of animation, special late-breaking deadline for Siggraph. And, prepare for BFA thesis review and show.

May 11-May 15th, 2009: Show final medical animation, with all post-production aspects. Send to the Cystic Fibrosis Foundation.

May 16^th, 2009: Graduate

Post-graduation: Apply for medical animation jobs.

Week 3 Story Draft

*Writing In Progress*

Co-Written By: Phoebe Ireland Coleman and Bill Elder

*Mostly described by Bill Elder. Actual animation narrative is being written and will be posted soon. Revisions will be done in dark blue.

CF Med Animation Story
January 30th, 2009

Cystic Fibrosis Medical Animation

Cystic Fibrosis is an autosomal recessive genetic disorder meaning it actually takes two copies of the CF gene to have Cystic Fibrosis. One copy of the CF gene and one normal gene means that the individual is a carrier. One of the explanations given for why CF still exists in the gene pool is that carriers of the gene may have a better chance of surviving a Cholera infection by decreasing the amount of water loss and preventing dehydration.

(see first set of images)

[Animation: Show Chromosome number 7, rotating into the scene, away from the camera. Landing next to the other chromosomes sets and adjacent to the other chromosome number 7. Labeling the first chromosome (on the right) as the chromosome where the DNA information would lie. Label right with “carrier.” If a person has two mutant genes, the person is diagnosed with CF.]

The CF gene codes for the Cystic Fibrosis Transmembrane conductance Regulator or CFTR for short. The CFTR is found on smooth tissue throughout the body, most importantly in the airways and the pancreas. The CFTR is an ion channel that helps move water into the mucus in the lungs making it less viscous and easier to clear from the airways. While there are numerous mutations in the CF gene they all lead to a dysfunctional CFTR that is inable to pump ions across the membrane onto the surface of the lungs. This dysfunctional ion channel (CFTR) leads to mucus that is too thick for the cilia to move out of the lungsand the mucus builds up.

(See second set of images)

In the lungs this thick mucus become a problem when bacteria manages to make it's way inside the mucus. The mucus acts as a sort of "bio-dome" for the bacteria allowing it to colonize the lungs. Once a bacteria (most commonly Psuedomonas, although very rarely and very dangerously B. Cepacia) manages to get inside the mucus the body will send white blood cells (lymphocytes) to kill the bacteria, but the chemicals produced by the white blood cells will be blocked by the thick mucus and will instead destroy the surrounding lung tissue. The bacteria itself also damages the lung as it grows.

The majority of CF research is focused on clearing mucus from the lungs because nearly all patients die from some form of lung infection (or conditions associated with it.) As a result the majority of CF treatment is focused on the lungs. Pulmozyme is a nebulized medication which is actually an enzyme which breaks apart DNA. As it turns out the bacteria leaves strands of DNA in the mucus which make it much thicker. By breaking this DNA up into smaller bits it makes the mucus much less viscous and it can be coughed up by the patient using the Huff Cough Technique: http://www.sierrabiotech.com/bt_copd_huff.html. Many nebulized antibiotics are also used help kill the Psuedomonas such as Tobi (Tobramycin for inhalation), Colistin, Aztreonam and a few more I can't remember. Along with inhaled antibiotics patients are often prescribed Ciprofloxacin which is in pill form and can be a very effective measure for fighting more serious infections.

Aside from antibiotics, many inhalers such as Atrovent, Serevent, Albuterol and Advair are used to help reduce the constriction and inflamation of the airways as a result of infection (Asthma.) Hypertonic Saline has also begun to be nebulized as treatment for CF. It is essentially really salty water and the exact mechanism of how it works is unknown (at least to me!) although it may help stimulate other ion channels to open in the airway. While a patient does a nebulizer treatment they will also commonly use "the vest". The therapy vest sits on the outside of the chest and inflates with air. It then inflates and deflates rapidly causing the lungs to shake and causing the mucus to be thrown off of the lung surface and then expelled. Along with this therapy CF patients should also try and stay active by running as often as they can. It is hypothesized that running may cause other channels in the airway to open up and help clear mucus.

In the pancreas the thick mucus can block the enzymes from leaving the pancreas and can over time begin to destroy the pancreas. This destruction can also destroy the Islets of Langerhans whcih produce insulin and this can lead to Cystic Fibrosis Related Diabetes (CFRD). This is why many CF patients must take digestive enzymes (the ones I take are called Creon) and why CF patients have a hard time maintaining their weight. Many individuals who have a more serious condition must have a feeding tube (called a G-tube) inserted into their stomach.

[Animation: A cross-section of the airway epithelia and the CFTR. I would then show that because of the lack of CFTR function the mucus becomes far more viscous and the cilia are unable to adequately move it out of the airway. Then you could show the colonization of the mucus by Psuedomonas and the resulting immune response which damages the lungs.]

Here's a site with some decent pictures of the CFTR: http://old.schoolscience.co.uk/content/5/biology/mrc/3/page3.html (It is actually far more complicated than that, it turns out it does a lot more than just let chloride through)

[Animation note: that the CFTR also causes problems with the formation of the vas deferens in males leading to infertility. Also the CFTR is present in sweat glands and as a result CF patients have much saltier sweat than normal, which is the most common means of diagnosis for CF.]

For the lungs you could show mucus accumulating over time and gradually turning from clear to yellow to green as a result of infection. You could then show how a mucus plug could block off one of the branches in the airway and how this could dramatically drop lung function due to the loss of volume.

[Animation: show mucus accumulating over time, with gradual color as a result from an infection. Change from clear, yellow, and ending with green.]

[Animation: show mucus plug block off one of the branches in the airway and how this could dramatically drop lung function due to the loss of volume.]

[End Animation: Show credits]

From the Cystic Fibrosis Foundation, Colorado Chapter Website: About Cystic Fibrosis

What You Need to Know

What Is Cystic Fibrosis?

Cystic fibrosis is an inherited chronic disease that affects the lungs and digestive system of about 30,000 children and adults in the United States (70,000 worldwide). A defective gene and its protein product cause the body to produce unusually thick, sticky mucus that:

• clogs the lungs and leads to life-threatening lung infections; and
• obstructs the pancreas and stops natural enzymes from helping the body break down and absorb food.

In the 1950s, few children with cystic fibrosis lived to attend elementary school. Today, advances in research and medical treatments have further enhanced and extended life for children and adults with CF. Many people with the disease can now expect to live into their 30s, 40s and beyond.

Symptoms of Cystic Fibrosis

People with CF can have a variety of symptoms, including:

• very salty-tasting skin;
• persistent coughing, at times with phlegm;
• frequent lung infections;
• wheezing or shortness of breath;
• poor growth/weight gain in spite of a good appetite; and
• frequent greasy, bulky stools or difficulty in bowel movements.

Statistics

• About 1,000 new cases of cystic fibrosis are diagnosed each year.
• More than 70% of patients are diagnosed by age two.
• More than 40% of the CF patient population is age 18 or older.
• The predicted median age of survival for a person with CF is more than 37 years.

The Cystic Fibrosis Foundation

Since 1955, the Cystic Fibrosis Foundation has been the driving force behind the pursuit of a cure. Thanks to the dedication and financial backing of our supporters--patients, families and friends, clinicians, researchers, volunteers, individual donors, corporations and staff, we are making a difference.

• Learn more about Testing for Cystic Fibrosis.
• Explore all aspects of Living with CF at every stage of life.
• See what Treatments are available and what’s in development.

Source: http://www.cff.org/AboutCF/

Spring 09- Week 1

This week, I am currently writing the story script and drawing out storyboards for this production. I will have medical illustration help from my father, who obtained his phD in Nuerobiology.

For the senior production class, we must submit an outline of our production and demo reel goals by this Wednesday. With that outline, I will add more dates and deadlines, including summer internship application deadlines, and post them up here.

Pre-Production- Step One: Creating the Story and Goals

Today marks the first day that I am commencing on a medical animation short for my undergrad BFA thesis. I am working with the Cystic Fibrosis Foundation, Denver Chapter so that I can accurately represent a working digital animation of symptoms and affects of Cystic Fibrosis.

Dates and Goals:
January 2009: Start preproduction and complete storyboards, script, and all other pre-visualization aspects.

January 23, 2009: Start animation

February 18th, 2009: Poster of a work in progress animation submitted to Siggraph 2009 Student Poster competition

March 2nd: 80% of the production complete to submit the animation to the SIGGRAPH 2009 Student Competition

May 6th, 2009: Optional- Poster of animation, special late-breaking deadline for Siggraph