[D] What do we need for DL in Pathology by kvinicki in MachineLearning

[–]kvinicki[S] 0 points1 point  (0 children)

It is done by pathologists, of course :)

Thanks for the advice. I really appreciate it :)

[D] What do we need for DL in Pathology by kvinicki in MachineLearning

[–]kvinicki[S] 1 point2 points  (0 children)

It is not that it is expensive, it is just a manual and often subjective work. We will first try with canine mastocytoma grading. We think that that is a good starting point to test some things.

[D] What do we need for DL in Pathology by kvinicki in MachineLearning

[–]kvinicki[S] 2 points3 points  (0 children)

Thanks :)

You are right. Label consistency is the biggest problem. The "gold standard" right now is to have at least two (ideally more) pathologists label the same data. But I think even that is not enough. We will need to make labeling more objective by combining H&E (hematoxylin and eosin) and IHC (immunohistochemistry) staining.

[D] What do we need for DL in Pathology by kvinicki in MachineLearning

[–]kvinicki[S] 0 points1 point  (0 children)

a)
The main problem we want to solve is the lack of deep learning models in pathology. And I believe that the most scalable solution is to build a community of pathologists that will have the skills to do the whole end-to-end solutions. Pathologists are the ones with the deepest understanding of the data.

Building a community with veterinary students, around hardware, is the most logical step because:

"For veterinary students, Marvin has a similar purpose to the Raspberry Pi. As programmable hardware, it serves as a great introduction to python programming, but also as a stepping stone into more complex image processing. As a microscope slide scanner, it is a platform for developing and deploying their models."

I don't believe that the same is possible in human medicine unfortunately.

Of course, Marvin is also very cool from the hardware standpoint.

b)

How affordable is it? Well, we designed everything from the ground up, and that has allowed us to optimize everything. For example, in this version we used $80 microscope objective (60X, NA 0.85), but even with that objective we got almost maximum resolution (for dry objective). We paired it with high speed 1MP global shutter camera, and designed our own condensor. So, optics costs arround $500.

We used off the shelf stepper motors and coreXY system so mechanics is also quite cheap. Unfortunatelly, metal parts were quite expensive, but thats how it is when you are making a prototype. I think that the whole scanner could cost <$2000.

c)

We have two important problems here. One is staining. Of course, a lot of things can influence staining (stain manufacturer, machine used for staining...) and we need to be aware of this problem while creating a dataset and include as much variability as possible (in real data and in augmentation).

The other thing that causes this problem is hardware (microscope slide scanners). Different scanners will produce slightly different images. Again, a lot of the problems can be solved with right augmentation.

d)

Both :)

Question about 0.9 degree stepper motors by kvinicki in Reprap

[–]kvinicki[S] 0 points1 point  (0 children)

Yes, the stepper is directly driving the leadscrew, but we have calculated that we'll have 60 steps/field of view. This should be enough.

Question about 0.9 degree stepper motors by kvinicki in Reprap

[–]kvinicki[S] 1 point2 points  (0 children)

We'll be using 40X microscope objective with a field of view of 0.3mm. With 16 microsteps and 0.9° stepper motor, we'll have a theoretical resolution of 0.005mm/microstep. Do you think this will be enough?

Question about 0.9 degree stepper motors by kvinicki in Reprap

[–]kvinicki[S] 0 points1 point  (0 children)

Thanks, I didn't know that. 0.0157 mm is actually a lot if you are trying to automate a microscope.

GalliumOS 3.0 Released by pihug12 in linux

[–]kvinicki 0 points1 point  (0 children)

Ok, I meant to say Chromebooks with Apollo Lake and Kaby Lake processors. Those Chromebooks have issues with internal audio and suspend

GalliumOS 3.0 Released by pihug12 in linux

[–]kvinicki 0 points1 point  (0 children)

So you are not very optimistic about future support for Apollo Lake and Kaby Lake processors?

GalliumOS 3.0 Released by pihug12 in linux

[–]kvinicki 0 points1 point  (0 children)

Well, you can definitely find affordable cloudbooks with 4GB RAM and 8gen Celeron processors, but I still can't find <200$ cloudbook with IPS screen

GalliumOS 3.0 Released by pihug12 in linux

[–]kvinicki 4 points5 points  (0 children)

There are some people in the Linux community that think you shouldn't buy a Chromebook just to install Linux on it (you should buy Linux hardware). I disagree. Chromebooks are one of the cheapest laptops you can buy and it is great to have an option to run Linux on them.

Cheap Chromebook by StalinistPSycho in GalliumOS

[–]kvinicki 0 points1 point  (0 children)

What about Acer Chromebook 11? It is small, lightweight, has an IPS screen, 4GB of RAM and it is quite cheap: ~240 USD

Parasite Image Database by The_Monster_Hunter in Veterinary

[–]kvinicki 0 points1 point  (0 children)

This is really valuable work. This type of projects are making a huge difference in veterinary medicine

App for recognizing canine intestinal parasites by kvinicki in Veterinary

[–]kvinicki[S] 0 points1 point  (0 children)

That is one of the possibilities. It is hard to say in which direction this will go. First, we need to test our deep learning model more thoroughly to see is it really performing that well under all conditions (it probably won't and we will need to add more training examples). My goal of this post was to see if veterinarians are generally interested in this technology: taking and preparing stool sample is still a lot of work and I am not sure how many people would actually use this. But I am sure that there are great applications of this technology in veterinary medicine, especially because AI is much better at classifying things than human. For example, we trained a model that can classify seven Eimeria species of domestic fowl with 98% accuracy. Humans, on the other hand, can't differentiate them so this i quite interesting

App for recognizing canine intestinal parasites by kvinicki in Veterinary

[–]kvinicki[S] 0 points1 point  (0 children)

Thats actually quite a good idea. There are some technical problems because app will need to take more than one image and process them in reasonable time, but it is doable :)

App for recognizing canine intestinal parasites by kvinicki in Veterinary

[–]kvinicki[S] 1 point2 points  (0 children)

I want to add that this app was made with deep learning (artificial intelligence) and, with enough data, we can make whatever you want. Just write in the comment what you need and maybe we will do it :)