These questions were answered live in the Q&A. You can also view these responses in the recording.
Question: Are images available at different resolutions?
Graham (in chat): 3D volumetric images are only available in the resolution at which they were collected from the scopes. The images in the web browser are often downsampled, but if you download the 3D images, they are all full resolution ome.tif files that can be opened in programs like ImageJ, ChimeraX, or our own desktop viewer AGAVE. We are working on collecting images a multiple resolutions and even “predicting” higher resolutions using deep learning, but it will be awhile before that becomes available… lots of validation/testing to do.
Question: Eric; do you distinguish between mitosis and cell division (cytokinesis). For example, liver cells are often binucleated. Does the Allen Institute have liver cells and other “odd-ball” tissues?
Eric: In my coursework, I do distinguish between cell division, mitosis, and cytokinesis, and we use the Drosophila embryo epidermis as an example of cell division without cytokinesis. Cytokinesis doesn’t show up in these images, so it’s not one of the stages that students can look at.
Graham: At the institute we’ve decided to focus only on one differentiation protocol and that’s to cardiomyocytes. We want this to be a template, where we will provide the methods for other labs to do their own differentiation into other tissues. We do not have liver, but we do have the cardiomyocyte data coming off the pipeline now and we’re working on ways to analyze it and provide it to the community, the way we provide the data on the human induced pluripotent stem cells in their colony state.
Information on the cardiomyocyte project is available here.
Question: Are there virtual microscopes that student can use?
Graham: I’m not quite sure what you mean by virtual microscope, but if you mean a microscope that a student can control, we don’t have that. I think there are other websites that offer that. We have considered having streaming footage from our microscope that you could watch on a live cam, and if that’s something that would be interesting, we could provide it. But in terms of controlling a microscope remotely, we don’t provide that, or in terms of having a virtual microscope where you’re zooming into a 3D tissue, we don’t have that. We do have a project in development called Simularium, which will be a multiscale viewer, which will take you down from tissues to mechanical simulations of molecular interactions, so you can see how emergent complexity produces complex behaviors in cells, but it’s going to be a couple years before that’s at a level that’s useful to your students. We’ll have some previews coming up in the coming months.
Question: Does the cell viewer work on a tablet/ipad?
Dan (in chat): Cell Feature Explorer and 3D Cell Viewer are capable of running on tablets, as they are ordinary websites, but are not specifically designed for small screens or touch interaction. Your experience will definitely be better on a laptop or larger screen. We are working on designs to provide mobile-friendly experiences with the Cell Feature Explorer.
Graham: I’ll quickly say that the 3D Cell Viewer that Eric uses in his demo functions, it’s not an optimal experience because the window for where you would do the counting is relatively small. The Cell Feature Explorer also functions, but the plotting interface is also relatively small on the screen, so it’s not very useful yet. This is a priority for us to develop later in the year, but I’m really curious if Eric has experienced students trying to use it and having any success, or if they’ve always had to go to their laptop.
Eric: I can actually not share any of that because… I’m not aware of students using it. Students typically have not had technical problems, but I cannot tell you what they’re using to do it.
Graham: We’d love to hear in the forum if this is a major priority. For example, what percentages of students do you have in your classrooms who are using this type of devices?
Question: Does the Cell Explorer or other database at the AI include ultrastructural details? i.e. TEM, immunoEM?
Kaitlyn: I will chime in and say that the Allen Institute for Brain Science does have an EM project, but they haven’t released the data from it yet.
You can read a story on the Allen Institute website about the neural tissue EM project.
Graham: On the Cell Science side, the Cell Feature Explorer doesn’t have a connection like that, but some of the other tools such as the Visual Guide to Human Cells include some classical electron microscopy imagery that comes from the textbook world about what these structures look like at this resolution, as well as illustrations from the protein data bank about what the protein structure and the macromolecular structures look like, so we’re talking alpha tubulin-beta tubulin dimers and how they relate to whole microtubules. Again, we’re looking to start filling in the multiscale view of whole cells with the Simularium project, where we want to integrate image data with modeling data into a comprehensive virtual cell. And again, that’s going to be a long term project, but keep your eyes out for some previews of it later this year.
Question: Does Allen Institute ever use Zooniverse or other citizen science online platforms to crowdsource interpretations of cell observations over many cells or tissue types to help inform the scientific research at the institute?
Kaitlyn: For the Allen Institute for Brain Science, some of their 3D neuron reconstruction data is available through a platform called Mozak, that enables people to trace the neurons in 3D, and that data does get fed back to the institute. That’s an Allen Institute for Brain Science resource. It’s using a different data set than we were covering today, but may still be of relevance to your classes.
You can find Mozak here.
Graham: This is a very timely question because we have just started talking to the developers of Zooniverse. We are testing how we can use it not only for citizen science but even as a powerful tool at the institute for doing some of the image quality, image sorting, and annotations in an efficient manner for our scientists and then we want to eventually try to compare that to citizen science methods.
Question: Is it possible to see mono-oriented chromosomes. Later clarification: Chromosomes that are attached to only one pole. AO is measured from time the last chromosome start to congress.
Eric: The answer is probably no, because the images are good enough resolution to see stage of mitosis, but not good enough to see individual chromosomes.
Question: I love the available data and the mitosis lesson plan. What other lesson plans are you working on, or any ideas you’ve had that we might be able to run with on our own?
Kaitlyn: At alleninstitute.org/learn, we have a couple of additional lesson plans besides Eric’s, we have a couple that were developed at the Allen Institute, that I worked with some of our scientists and we have those available, and we have a couple that were developed outside of the institute, we have one Brain Science one and two Cell Science ones. If you do use the resources in your classroom and you write it up publicly anywhere, whether it’s in CourseSource or another forum, please shoot us an email at firstname.lastname@example.org to let us know.
Graham: I want to add that at the Allen Institute for Cell Science, none of us are teachers, we’re biologists and engineers. We rely on teachers like Eric and Carlos and Tom to come to us to tell us how they’re using these tools. We’re very interested in ways that we can modify or test or develop these tools for educational uses. If there are successful uses out there like the one Eric demonstrated today, we want to help amplify that and get it out to as many people as possible. We’re really interested in hearing more from you on the forum.