image timeline

[lizzieinvancouver]

I am working on tasks for folks this summer and wondering when we may have test images, especially of multiple cores together .... @DeirdreLoughnan Do we have enough cores to set up a full tray? If not, can we strategize about making this happen. @afong3 If we did/do have cores do you know when any test images might be ready for @sandyie ? I'd also be interested in when we might get our cookies from the common garden photographed. I understand we are a ways off a fully functional way to get the images, so wondering especially here about any hacks to get some images sooner?

[afong3]

I definitely see the need for some test images and have been thinking a bit about how to do this while still making fruitful progress on the project as a whole. I've come up with a hands on method to manually shift the core to get the images. This requires the big tripod in the lab and a bit of finesse. I just need to 3D print a couple of brackets (which I'm doing some tests on as we speak) and write a little bit of code to take the images with the Pi cam. I'm a bit strapped with finals until Wednesday but I'm aiming to have a couple of test image sets before May.

[lizzieinvancouver]

@afong3 This sounds great! Thanks for working on it and let us know how it goes.

[lizzieinvancouver]

Update from @afong3 over email:

[afong3]

After manually shifting the core underneath the microscope I have been able to capture two rows worth of the cookie. The steps were about 2-3mm so doing the entire cookie this way is a little tedious and I have a decent chance of making a mistake. I'll make another attempt in the coming days. Until then here are the images - please let me know if I've made a mistake in overlap or otherwise @sandyie.

[lizzieinvancouver]

@afong3 Thanks! Would it also be possible to take images of the core tray? I know it does not have many cores (I think @DeirdreLoughnan and I are working on that) but I understood it was a type of image that @sandyie was especially concerned about testing out ... and come this fall we will have lots of cores to sample. Thanks!

[afong3]

@lizzieinvancouver I can definitely get at least a set of a core. Does the black plastic tray work for the cores that you want images from? I can alter the model / print a new one as well.

[DeirdreLoughnan]

@lizzieinvancouver @afong3 I am wondering what sanding the printed mounts will be like. Most boards are designed so that about half of the sample is in the well and you simply sand flush to the board. Since they are made of wood it is not a big deal if you accidentally sand the board a bit, but would sanding the printed ones be an issue?

[lizzieinvancouver]

@DeirdreLoughnan Good question, but I have no idea! I think you may just have to try it.

@afong3 I think ideally one set of images of the black one and one of the wooden one (I saw it on the bench the other day) so we see how both work (as I think we will end up using both types).

[afong3]

@DeirdreLoughnan Sanding the plastic should be fine but this is a good point. If 3D printed core holders are the way to go, it would be important to make sure that we don't sand deep enough to get to the internal structure. This is easy to avoid by making the solid top layer thicker than default - I've made note of this for future reference.

[afong3]

@lizzieinvancouver @sandyie Taking images of the unsanded cores in the tray might be a lot more work than its worth. The microscope lens is very sensitive to even a mm difference in subject height and the variation in height across the length of a core on the current tray is approx 2-3 mm. If I were to take images across its length each image would have portions of being in and out of focus.

Considering this, @sandyie is the set of images for the in-focus cookie sufficient for the time being?

[lizzieinvancouver]

@afong3 Ah, good point. @DeirdreLoughnan says she will ask (one more time) for a sanded set we can borrow from another lab ASAP.

[afong3]

@lizzieinvancouver @sandyie I just recalled that CaptuRING authors have 15 or so samples published online as well. Some have more visible core holders than others - hope this can be of help.

[lizzieinvancouver]

@afong3 Thanks! That seems like a great plan ... I bet Griffin of gigpixel has some too. I could try pinging him again (he ignored me last time).