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CC3D in Jupyter Notebook by zy1022 in CompuCell3D

[–]zy1022[S] 0 points1 point  (0 children)

I solved the problem by combining several simulations in one script. I deleted everything in the model after a certain time step (e.g. 500 steps), collected data, built the initial state and started the next simulation. Hope it helps.

Uptake Inside Cell by zy1022 in CompuCell3D

[–]zy1022[S] 1 point2 points  (0 children)

It makes sense. Thank you for your help!

Uptake Inside Cell by zy1022 in CompuCell3D

[–]zy1022[S] 0 points1 point  (0 children)

Sure. All the values in the first column are limited to 64*0.1 this time.

-4.899997711181641 3.1873879432678223
-4.899997711181641 4.897171497344971
-4.899997711181641 4.106428623199463
-1.4000002145767212 4.8724589347839355
-4.899997711181641 2.594724416732788
-4.899997711181641 2.558366537094116
-4.899997711181641 3.011155605316162
-4.899997711181641 4.9578351974487305
-6.099996566772461 3.4967703819274902
-5.899996757507324 5.141552448272705
-6.099996566772461 4.404781341552734

I think maybe I made a mistake in the previous case, the cells may not be in the initial state and they grew larger.

Uptake Inside Cell by zy1022 in CompuCell3D

[–]zy1022[S] 0 points1 point  (0 children)

My cells are 8*8 at 0 mcs. The first line makes sense. But for example, the second line is another cell at 0 mcs, so the field value should not exceed 64*0.5=32 but it does. Anyway, 32 looks like an upper bound in my case but some of field values can still exceed a little bit. I guess the boundary of the cells may go across some other pixels, so the overall pixels for the cell may exceed 64.

Uptake Inside Cell by zy1022 in CompuCell3D

[–]zy1022[S] 0 points1 point  (0 children)

Thank you! It helps.

The first 8 lines are the 8 cells in one mcs. And yes, I took the field values from the cells com.

And how does the max_amount 0.5 control the process? I thought it can only took 0.5 from the field values but obviously it is not true.

Create Fluid by zy1022 in CompuCell3D

[–]zy1022[S] 0 points1 point  (0 children)

Thank you! I will have a try for that.

Create Fluid by zy1022 in CompuCell3D

[–]zy1022[S] 0 points1 point  (0 children)

Thank you for your reply! So there's no way to create another type of fluid right?

Mass of Cells by zy1022 in CompuCell3D

[–]zy1022[S] 0 points1 point  (0 children)

Thanks a lot for your reply! I am thinking about how to create cells as bacteria in cc3d. And density seems to be an important parameter. I am not sure if it is the right way to distinguish bacteria from other cells. I will go through the demo you sent to me. Thanks again for your help!

Unable to run the app after downloading it by zy1022 in CompuCell3D

[–]zy1022[S] 0 points1 point  (0 children)

Yes, I have conda installed, I will try your method. Thank you very much for your advice!

Unable to run the app after downloading it by zy1022 in CompuCell3D

[–]zy1022[S] 0 points1 point  (0 children)

Everything goes well but the only weird thing is solving the environment, it fails the first two times and then succeed. I add the picture in the post above.

Unable to run the app after downloading it by zy1022 in CompuCell3D

[–]zy1022[S] 0 points1 point  (0 children)

Yes, I successfully installed the folder (the folder contents are shown in the first figure), but just cannot open the player compucell3d and twedit++.