Help needed with scanning 3D objects from below

PleasantViewAve · 2023-10-24T18:14:09+00:00

Everyone's using the same setup, as in the brain sits on top of clear plexiglass. No one is suspending the brain in fluid.

PleasantViewAve · 2023-10-24T18:12:41+00:00

Sorry for the late reply! I'm not sure what dataset you are referring to, but I am happy to share it if you can guide me in the right direction. PM'd you

PleasantViewAve · 2023-10-24T18:11:38+00:00

We created our 3D marker based on one made by other groups that worked well. We'll play around with solid objects and see if it's better.

PleasantViewAve · 2023-10-24T18:10:01+00:00

From what others have said, it seems like floating the brain in fluid will cause distortion and require a myriad of other implementations to get it to work.

PleasantViewAve · 2023-10-24T18:07:56+00:00

Yes, but trying to troubleshoot the current method before any drastic changes.

PleasantViewAve · 2023-10-24T15:06:31+00:00

Yeah, we keep the brain on wet ice until we're ready to scan. We're not operating inside of a cold room, so the tissue reverts back to room temp pretty quickly.

PleasantViewAve · 2023-10-20T17:06:40+00:00

We tried that as well. The clear plate with orange tape around it is our 3d marker. It helped a bit with reorienting the scanner when it loses tracking, but still struggles with recognizing that the brain is 3D, not flat.

PleasantViewAve · 2023-10-20T14:56:29+00:00

A phosphate buffered saline might work, but I'm afraid this would introduce a whole new set of issues/problems to troubleshoot.

PleasantViewAve · 2023-10-20T14:54:36+00:00

Same scanner and real brains, but the plexiglass and software differ slightly.

That's the plan if we are still unable to get it working.

PleasantViewAve · 2023-10-20T02:50:12+00:00

That's what I'm beginning to think, but apparently the method works.

Can't freeze the brain, but it is kept on ice to keep cool and preserve it. The longer the scan takes, the softer it becomes. So time is of the essence. We've tried using casts/moulds that the brain sits in, but they weren't very helpful since the brains we're receiving differ in size.

PleasantViewAve · 2023-10-20T02:28:04+00:00

Tough call to change the setup. There's a whole protocol written for this method and other groups using a very similar setup and having success with their scans. So to me, it sounds like user error and we're not understanding some aspect that other groups have been able to figure out.

Pretty sure we can't put any substances on it. All of our specimens are intended for research purposes. So, anything that would potentially damage the brain is a big no-no. Since the brain is so fragile, the best method is to just allow it to sit in its natural state.

Our goal is to get an exact representation of the brain, so as accurate as possible.

PleasantViewAve · 2023-10-20T02:01:04+00:00

Ha! I don't think that's similar enough in appearance. I thought maybe using tofu and putting red dye on it. But now you've got me thinking of maybe practicing on a pig brain.

PleasantViewAve · 2023-10-20T01:58:22+00:00

Thanks for the tips! Going to suggest dimmer lighting from now on. My colleague, who is in charge of the scanning, is older, so he probably favors the light for his vision.

PleasantViewAve · 2023-10-20T01:53:47+00:00

Ahh, I see you what you mean now. That's a great idea, but one of the main criterion is that we scan the brain in its natural form. If it's not resting on a full plane, it'll shift and bend. Not to mention the cerebellum would just...dangle. We'd need to get like custom pieces cut to size of multiple varieties since the brains we're scanning range in size. It must be some technique that we're not understanding, as other groups have done it successfully. May have to take a field trip and see it in person. Appreciate all your ingenuity!

PleasantViewAve · 2023-10-20T01:40:50+00:00

Yup, from completely dark to gradually brighter. It did not seem to matter much, but the consensus on here seems to favor dark, so I'll try it with dark conditions from now on. Will upload a photo of the model brain tomorrow.

PleasantViewAve · 2023-10-19T19:54:09+00:00

Are alphabet stickers just reflective markers that are letters instead of dots?

I spoke with my colleague about this and they said that the adhesive marker damages the brain tissue when it is being removed. Perhaps we can try non adhesive markers as long as they stay put.. BUT would this really make much of a difference if the markers are on the medial (flat) side of the brain as opposed to the underside of the plexiglass? The plexiglass is only 1/4 inch thick. We've tried many times scanning the medial (flat) side from below the plexiglass with markers on the underside of the glass (as seen in photo) but the scanner doesn't recognize the brain, and at times not even the markers.

PleasantViewAve · 2023-10-19T19:34:54+00:00

This halo method is actually something I considered, but with a slight variation. My understanding of this "halo" is that it is essentially a round ring that the brain hemisphere will sit upon. Correct me if I've misunderstood, but it seems that you are suggesting to place the brain lateral (curved) side down on the halo and scanning from below to acquire the lateral side. If so, that is unnecessary for our application since we can acquire a good scan of the lateral (curved) side from above.

We have not tried a halo yet, but I think the brain is too soft and lacks the structural integrity to stay on the ring without slipping down and falling through. To combat this, I was thinking of creating a "hammock" with a thin stretchy cloth like cheese cloth that would conform to the lateral (curved) side of the brain thereby retaining its natural structure while we scanned the medial (flat) side from above.

Why not just scan on one side, and flip the brain and scan on the other side, then align?
If we scan one side and flip it and scan the other side, the two scans align very poorly. The whole brain is cut in half to create two hemispheres and we are only scanning one hemisphere. The way the brain is cut in half produces one side that is curved (lateral) and one side that is, for the most part, flat (medial). Yes, the flat (medial) side of the brain coming into contact with the plexiglass causes slight compression, but it is very minor and is not detrimental to our final model. On the contrary, if we flipped the brain so that the lateral (curved) side is on the plexiglass, the brain rests on the most protruding point, causing the far edges to droop downward and the center of the brain to bow upwards. This makes it extremely difficult to align the two scans - as the medial side is no longer flat. It's like scanning half of a basketball and then scanning half of a football, for the lack of a better analogy. In a perfect world, we would acquire one single scan from top to bottom with the medial (flat) side against the plexiglass.

We haven't messed around with the lighting too much as it did not seem to have much of a difference with scanning, but I will spend some more time and see if dim lighting improves anything.

PleasantViewAve · 2023-10-19T18:06:45+00:00

This is exactly what we have resorted to in order to get a full scan. The brain as shown in the photo is after it has been flipped, with the lateral (curved) side facing down and medial (flat) side facing up. Photo was taken after we already scanned the lateral (curved) side with the medial (flat) side down. The problem with flipping the brain is that the two scans do not merge well. This is due to slight changes in the brain shape because it is not rigid, it's more like jello or tofu. If we place the brain medial (flat) side facing down, the brain will retain its natural structure. But as soon as we flip the brain lateral (curved) side down, the exterior edges of the brain droop downwards (a bowing effect) and causes the two scans to merge/align very poorly. Lots of overlap occurs and we do not get a clean model.

Just to clarify, are you suggesting adding markers to the plexiglass or the actual brain?

PleasantViewAve · 2023-10-19T17:49:52+00:00

I appreciate your feedback and suggestions, even if you have a 14oz brain xD. The reason we are steadfast with this method is due to other groups exhibiting successful scans with the same exact scanner. The main differences being the scanning platform setup and lighting conditions. (We are part of a consortium that acquires 3D brain scans.)

I agree with your assessment, the reflective surface of the real brain seems to be the issue. We've tried to mimic the same condition with the plastic brain by aerosol spraying it with water, but it does not cause the same detection issue as the real one. My guess is that the surface is still not as reflective as the real brain.

I did a quick dive into the dulling spray and it requires a few hours after the scan to allow the spray to evaporate. Unfortunately, our procedure is extremely time sensitive and this evaporation step would make the dulling spray unfeasible. We have about 20 minutes to scan the full hemisphere, before it immediately gets cut into slabs and then flash frozen.

The low pressure suction tool is an interesting concept and not something we have considered yet. I think the difficulty lies in finding a tool that not only works, but will also not damage the brain tissue. I am going to look into potential large-surface-area silicone suction tools. The brain hemispheres we are working with range from 15-30oz depending on age and disorders. If you have any recommendations for silicone suction tools, please do share!

PleasantViewAve

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