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Oct 12, 2020

could not load tiff sequence for volume rendering

Hi I am new user of Aivia community free software. I am trying to load my tiff sequence of fluorescent image and try to volume render in 3D. I load the tiff sequence by File -->import --> image sequence. I can see my loaded image file in the workspace at the botoom. But it's in one slice only. There is no scroll bar to scroll through the different slices and I also could not see the volume. I can see only empty bounding box. Please see screen shot. I am not sure any step I miss to load tiff sequence and render 3D.

Thank you

Win

12 comments

12 Comments

Luciano Lucas

Oct 16, 2020

Hello Win,

Thanks for checking out the issues. Aivia does need the GPU with dedicated (on board memory), specifically an NVIDIA card. Out testing with Quadro cards is limited as they are much more expensive and in terms of performance for rendering they are not noticeably better than the non-Quadro card. Personally, I am using a RTX 2080 and it is great.

So, the first step is to assign then NVIDIA card to Aivia (I know you mentioned it crashes). Then ensure the drivers for that card are up to date. You can use the NVIDIA drivers web page to check that. Looks like the latest for the P2000 (on windows 10 64bit) is from September 30th (2020):

https://www.nvidia.com/Download/driverResults.aspx/164732/en-us

Then, restart the machine. After the restart make sure that the NVIDIA card is still assigned to the NVIDIA card.

Now, try Aivia again. Let us know what you see.

Luciano Lucas

Oct 21, 2020

Replying to

Copying (with Win's permission) his replies:

From: Win Min Tun Sent: Wednesday, October 21, 2020 8:30 AM

Subject: Re: data file from Win - aivia community forum

Hi Luciano

Ignore my previous comment about the color channel as I know how to add the color now.

But just wondering if the two image volumes with different color channels can overlay in Aivia. I have blue and green (attached).

I see some Aivia tutorials on youtube. It seems to me that I have to overlay different color channels prior to loading to Aivia. Anyway, that's not a problem for me.

Thanks

Win

On Wed, Oct 21, 2020 at 10:47 AM Win Min Tun wrote:

Hi Luciano

I saw your video of my dataset in 3D on Aivia community forum and that looks great.

Thank you for the new Aivia version.

I installed and tried the 3D and it works well. Please see attached photo (the one and 2D and the other in 3D). I run this with NVIDIA card, but I found it is also working with the other card too.

Btw, they are in gray scale, not green channel. Do I miss any tab to turn on to get the correct color?

Thanks again

Win

Luciano Lucas

Oct 21, 2020

Replying to

Hi Win,

You are welcome. Happy it is all working out now. About your open question: "But just wondering if the two image volumes with different color channels can overlay in Aivia. I have blue and green"

Yes, this is certainly possible. Do this:

1) Use the File Import function to build the 3D data set (as you have done).

2) Delete any unwanted channels (right click on the unwanted channel and "delete")

3) Save the imported file as aivia.tiff.

4) Right click on the channel and choose Insert or Add Channel

5) The right click on the new channel and choose Load (then select your file with the second channel you want to load in). Make sure each file you use to Load includes a single channel.

More on the general functionality of Import Sequences of images: https://drvision.atlassian.net/wiki/spaces/AW/pages/254869670/Import+Image+Sequences

win min tun

Oct 22, 2020

Replying to

@Luciano Lucas Yes, that works perfect to overlay two differnt volumes. Thank you!

Luciano Lucas

Oct 12, 2020

Hi Win, it looks like Aivia has correctly read the images in but is not rendering them in 3D. To double check that the file did load correctly please look at the 2D View (called Main View) - see top left of the pic. below.

Once you are in that view you should be able to review all the slices in your 3D data set using the control below the image window (see picture below).

Assuming you can see the 2D slice and go up and down using the highlighted slider; please check this post: https://www.drvtechnologies.com/forum/aivia-community/i-have-issues-with-3d-rendering-software-crashes

That post covers the key reasons for why the 3D rendering may not work. Please us know what you found. Also, if possible please share the data set you have had problems with so we can try to replicate the issue and provide a more specific solution.

All the best

Luciano

win min tun

Oct 14, 2020

Replying to

Hi Luciano

Thank you very much for your reply. I followed your adivce and found that the files are loaded correctly and I can scroll the 2D slices by slider bar, which looks fine. But i noted that the images are in gray scale (should be green channel, not sure why not green). About the 3D rendering, I read through the link you provided. I have two GPU and I thought I have enough memory. Please see attached photos. I assign Avia to Intel (R) GPU as if I assign to NIVDIA, the software cannot load even 2D slices (it crashes instantly whenever i load the file).

So, I am not sure why I could not render 3D while I have enough memory (I think), and also conneted to internet. And Aivia is set to use a "Large Working Data Working Folder" (please see photo). But i use on my laptop, not on PC. Does it matter?

Thank you

Win

Luciano Lucas

Oct 16, 2020

Replying to

@win Also, if would be great if you could send me your log file. To find it go to File>Options. Then go to General>Logging and Open the file. Then save it and post here.

could not load tiff sequence for volume rendering

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