More elbow room in Box

Images for the onion test are being transferred to “the Box” on my university webspace account (they are retiring the old Goliath server and transferring to the new “Box.com” system this summer, so I figured I’d make the switch right away instead of waiting until summer. The Box has 10GB of space, which also facilitates things… the entire onion file is 1.12 GB and did not fit on the mywebspace).

At home the upload speed of my connection is 2.5 Mbits per second, so I am heading to the library for a few hours to hopefully take advantage of the faster time and avoid waiting 14.5 days for an upload that is just another test image. My computer is slow, my connection is slow, that’s life, so I am doing what I can to facilitate this process.

EDIT: already so much faster!
EDIT EDIT: well, not that much faster… JPEG might be the way to go for test? smaller sizes?

Screenshot 2014-03-02 12.31.58

For the final, I am re-doing the main outline to clean up some areas, since every detail really shows up in the large zoom. As I am working on the cell detail in the root area, the main drawing is wibbly enough that it requires some smoothing.
The brushes in Photoshop seem to favor a hard brush rather than a touch=sensitive one for the really close up shots, just to maintain a consistent line for cell walls.

The UW Botany dept is very generous with their time and resources, and I will be using their high-quality scanner to get cross-section images of my onion once it has started to sprout. They have many slides of root cell samples, which have been very helpful with that area of the drawing, but the leaves will have to wait until I have a sample to section and view… so I am growing one.

In the meantime, I am working on the overlaying images for a cricket (Order: Grillidae) based on drawings made during our cricket dissections in Entomology – including transparent underlays of the main outline and other organ systems so that it is easier to see how each organ interacts with other systems.

(image to be added later tonight)

Aspects I would like to figure out:
Lables: how to include them so they link to certain areas of the image and stay within the viewing frame. Most of the Google Maps information talks about linking to atlases, and has good information about creating point labels, but I’m still a little unclear about creating your own specific “street names” (in a manner of speaking) for the parts of the drawing.
Layers: Make it easy to switch back and forth between organ systems at various levels of zoom without having to start at the beginning. The developer page of google maps has some good information on this.

How to feel like a complete idiot:
Attempt doing simple tasks in a medium you are entirely unfamiliar with.

How to learn new things:
See above.

Maps and Tiles

The files for the project are quite large, it takes about 5 minutes to save the largest files. (I know, I know, of course a 32k x 32k image is going to take a long time, what did you expect? Well, I expect my computer to be magical, that’s all. The images for various zoom stages are composed separately (using the same outline as the basis to maintain consistency) and I will be substituting more detailed renderings as needed for the appropriate levels of magnification. I had them grouped as layers for a very short period of time, until it was clear that additional layers seemed to exponentially increase the time required to save my file. This may seem like child’s play to an experienced programer, but I am enjoying learning about it.

In order to be most compatible with the google API, the images are made with these particular pixel dimensions:

256 x 256 ——— 1x magnification
512 x 512 ——— 2x
1024 x 1024 —— 4x
2048 x 2048 —— 8x
4096 x 4096 —— 16x
8192 x 8192 —— 32x (slightly smaller than the 40x equivalent magnification
16,384 x 16,384 — 64x
32,768 x 32,768 — 128x (slightly larger than the 100x equivalent magnification)

I do realize these won’t be precisely accurate, since the first onion image is not exactly at life size – but the 1024 size gets closer to the actual size so I am rounding the estimated measurements up one degree (so the 16,384 is closer to the “40x equivalent”, and the 32k image will be rendered slightly smaller than “100x equivalent”). This should not be an issue for the cricket and for the Paramecium, since the 256 x 256 should be more than enough space for “life size” (a single slide, in the case of the unicellular organism). For larger life forms in the future, these measurements will be adjusted accordingly.

Prof. Kevin Ponto found software for splitting images into ready-made tiles for use in Google Maps API formats: Maptiler Free online, which promises incredibly quick working time: (2 minutes as opposed to 122 minutes, and half the finished file size). This program has very good prospects but is limited to 10,000 px images and it leaves a watermark on the image that is tiled. I will try this one to see how it compares to another free version from Mike Courturier: Tile Generator – test map loading this weekend, hopefully.

Maptiler Start: The next level (costs ~$28 USD, not bad) does not put a watermark on, but it is still limited to 10k pixels and requires(maybe?) 2 CPU cores. That end size will bring us to approximately 40x zoom, which equates to the lowest lens on a standard compound microscope. I have been developing the drawings at 32,768px, which gets me slightly above 100x magnification, which would be ideal. The highest level of magnification would be 400x magnification, but that may be reserved for the Paramecium… (which I probably should have started with, being a single-celled organism…)

Maptiler Pro: The next (and most expensive level at ~$560 USD) offers unlimited size, so I could get the zoom I want, but in addition to the hefty price tag it requires (maybe?) 4 CPU processors.

I think I’m willing to wait a few hours for images to tile. We’ll see though, perhaps a step up would be worth it.

Also posted on jwhisenant.wordpress.com

Conversations and Reference Sources

I have had several helpful conversations over the past week, and there have been many good thoughts and suggestions regarding this project.

Kandis Elliot – Scientific Illustrator: Botany Dept./Zoology Dept. 
Kandis had lots of advice and was very generous about sharing her process when approaching scientific illustration – after meeting with her I immediately went and made a reference sheet for Photoshop keyboard shortcuts (I knew the basics, but when you are able to fly through the toolset, it cuts your work time down significantly). We talked about information design, image rendering, and dinosaurs!

Sarah Friedrich – Scientific Illustrator and Media Specialist: Botany Dept.
It was very fun to speak with Sarah (after I went to the correct floor…) It is incredibly helpful to explain the scope of a project to different people, even just to articulate my own thought process out loud, as well as hearing alternate perspectives. We talked about layers of design (especially for organisms with multiple systems to represent: digestive/nervous/endocrine/etc) and were tossing around ideas of how that might be approached as a layering process to integrate the system representation, or if they would be completely separate.

Mike Clayton – Photographer/Collection Manager: Botany Dept.
An incredible resource for imaging suggestions – and generously offered the use of the Botany Dept compound microscope with a screen viewer, on Fridays. In addition to the comprehensive resources of the UW, he recommended looking for existing slides from Ripon Microslide for any specific botanical material. He has also compiled some fantastic images of plant material using a nice quality flatbed scanner (one of the many helpful tips: for 3D objects that you don’t want smashed against the glass: scan with an open top in a dark room – the resulting images are dramatically lit with a deep black background).

Some images from the UW collections: excellent reference points for 40x versus 100x magnification. Right now the only available slides are of root tips, so I am growing an onion from a common bulb in order to get leaf cell samples… (I had one in the kitchen but my industrious housemate discarded it… oh well) For the actual rendering, I am drawing one root’s worth and use it for the other root tips as well, adjusting for different curves, etc).

Image from UW Botany Department, scanned by Mike Clayton

Onion_UWBotanyDept_AlliumRootMetaphaseSpindle

Marianne Spoon – Chief Communications Officer, Science Writer for the Wisconsin Institute of Discovery
We met to go over the scope and plans for this project. Marianne had some great presentation format suggestions – I had been focusing mainly on the individual images but she was talking about how viewers might encounter the image options on a hypothetical website (i.e. possibly in a compiled image with hotspots on an where people could click on an onion/cricket/etc and then go to the zoomable map view. She was also wondering if the image would go even farther out, zooming out to a room, a building, a country, a planet. Perhaps something to consider in the future – maybe seamlessly link to a separate zoom map, since my files are getting quite large just from a “lifesize” viewpoint! She made me really start thinking about the larger integration of these anatomical maps into their intended application or something that I might not have anticipated!

In other news, I have several reference drawings from our entomology lab cricket dissections last week, so I have started compiling initial sketches of the internal systems for an upcoming map.

(also posted on jwhisenant.wordpress.com)

Frontier Fellow Project: In Focus Anatomy

In Focus Anatomy (working title)

Through the Wisconsin Institute for Discovery, I will be developing anatomically accurate drawings that will be structured with a “google-map” type of interface, functioning as a virtual microscope. This interactive educational tool will allow the viewer to zoom in to the cellular level on a variety of contrasting organisms, encouraging an active investigation of various life forms.

First image in progess: Onion (Allium)

Start out with basic drawing, then use the outline to guide the higher-detail and the cellular level stages. I will be visiting the Dept. of Botany’s collection in the next few days to look at Allium root slides for reference, to ensure a more accurate depiction of cellular construction.

Project in development: test map will be up very soon!