Luckily I am no longer pregnant. Huge thanks to the fantastic Sam Bond for making this illustration when she was procrastinating one day.
Learning a new program or technique can be expensive, especially if you’re just starting out in a new area of our diverse field. Why throw money at expensive programs, resources and tutorials when there are plenty of cost-free alternatives to get you going? With so many freeware programs to choose from, build the digital skill set that makes the most sense for your learning style and business!
But first, how do you find and use open-source programs? Check out the website alternativeto.net, where you can type in the name of a paid program for which you want to find an alternative, and then filter by open-source programs. It doesn’t have everything, but it’s a great place to start.
Next, you’ll want to find tutorials. Don’t just go poking around in a program because you might write it off for not feeling like what you’re used to with the paid version. Also, find tutorials that will teach you something a little outside of your comfort zone. To find these tutorials, I recommend checking out:
The host program’s site
Sites dedicated to tutorials in that program
Youtube/Vimeo
Learn a specific task with a cool result. Understanding the User Interface (UI) is great and all, but making something cool that you can be proud of is better. Put your explorer hat on and get excited about learning this new program! Also, don’t be on a time crunch- dedicate time in your business to learning new programs, it will pay off later.
Then, take notes! If this molecular visualization program can pop out a virus easily, you’ll want to document how you accomplished the task so that you can easily repeat the action when you are on a time crunch later.
Finally, you’ll have to decide what programs are still worth paying for, and that can change based on your particular business. Some programs simply cannot be replicated in the way you might need them. That said, watch for discounts. I saved $200 by buying the “old” version of a program, but it came with a free upgrade for the “new” version! That said, buy as you go. If I had purchased every program/plugin I wanted when I first graduated, most would have been obsolete by the time I used them. Wait until you have a project that will really sing with it, and then spring for the purchase.
Here are a few of my favorite open-source programs:
RadiANT:
Let’s say you want to make a 3D model from DICOM Data like CT or MRI. That’s called segmentation. There are a bunch of programs that can do that for you but if you were to open all the DICOM series on a disc into a segmentation program at once it could take a while, or even make your computer crash.
If you open the data first in RadiANT, you can see all these DICOM series on the left:
Use RadiANT before your DICOM segmentation program to speed up the segmentation process.
RadiANT cannot isolate 3D models, but you can quickly see which data sets look good enough to import into a segmentation program for isolation. Look at the slice thickness on the bottom left (thinner is better) and get a 3D preview using the button up top.
RadiANT does not currently make exportable 3D models from DICOM data, but can give you a quick sneak peek!
Now for our purposes, say I want to isolate the bones of the arm and hand. This guy has no hands! So I don’t want that data. We can check another series, and this guy has hands. That’s the data I want, so now I can take note of the data series title and import JUST that series into a segmentation program like InVesalius.
Don’t waste time and computing power: only pull the data series you want into your segmentation program.
This saves time, as many of the 3D segmentation programs can be a bit clunky. (I say this with love)
Invesalius:
InVesalius is a great open-source program for segmenting 3D models from DICOM data, especially if you’re trying to get bones out of CT Imagery. Here, I can upload just the data series I want to segment, and the program knocks out an exportable 3D model faster than it would if I had uploaded everything on the DICOM disc.
InVesalius is an open-source 3D segmentation program.
Google Unpaywall:
Google Unpaywall is a Chrome browser extension. Let’s say you’re doing primary literature research and you come up against a paywall. Google Unpaywall searches to find whether that same paper is available for free somewhere else on the internet. If the lock on the right is green, you can click on it to go to the free version of that paper. (Many thanks to UT Bioscience Librarian Porcia Vaughan for telling me about this one!)
The Google Unpaywall extension for Chrome Browser is completely free, legal, and only searches papers that fall within publisher permissions.
Open-Source Program List:
The below list contains links for several open-source programs, and several include a note on how I like to use them. With all of these, be aware of copyright restrictions, and cite the programs appropriately. Please feel free to contact if you have any favorites you don’t see here, and I’ll add them to the list. Happy hunting!
3D Modeling/Animation
Blender (BforArtists) is a fork of Blender with an artist-focused UI
Sculptris is a clay-based 3D modeling program (Zbrush-like) but was last updated in 2011
MakeHuman (character creator)
MeshLab (modification of 3D file types for import)
DICOM Segmentation
RadiANT is a DICOM viewer
Osirix (Macs only)
ITK-Snap (I personally like using this one to segment a brain or white matter from MRI data)
Photogrammetry
(This means taking multiple photos of a real item in the world, and using one of the below programs to make a digital 3D model composited from those photos)
Interactivity/Development
Illustration
Audio/Video Editing
Office Programs
Google suite (sheets/docs/slides/drive are available with a free Gmail address)
LaTex (scientific document preparation)
Project Management
Molecular Visualization
The Protein Data Bank allows users to see the 3D structures of molecules, but in order to export the structures for use in animation, an intermediary program must be used. These programs have different strengths!
Jmol (I use this one for chemicals that I can’t find elsewhere)
UCSF ChimeraX (I like this one for viruses)
Bioblender (molecular viz for Blender)
Avogadro (molecule builder)
CellPaint (huge thanks to Dr. David Goodsell for telling us about this one at AMI!)
Protein Imager (does not seem to have export ability)
RCSB (The Protein Data Bank) also keeps a list of molecular visualization tools
Plugins
Plugins are code that you can add to a program (paid or open-source) to add functionality
After Effects Plugins:
Videocopilot.net (this one is great for tutorials too!)
3DsMax Plugin:
tyFlow is meant to completely replace Particle Flow
Research
Radiopaedia helps users understand radiographic data
DICOM Repositories
Note: a lot of these programs build their bases by being free for a period of time, and then charging a premium for upgrades or new users. If any of these programs start to charge for the basic (read: useful) packages or become otherwise annoying/spammy, please let me know so that I can remove them.
A huge thank you to Sam Bond for the idea/title/pregnant Mellie illustration! Many thanks also to Neil McMillan, Donna DeSmet, Liza Knipscher, and Craig Luce for their open-source program suggestions!