NITRC QuickNII - Serial section aligner to volumetric atlases Forum: general

RE: Export original 2017 Files

Jacob Bumgarner — Thu, 14 Oct 2021 15:58:46 GMT

Fair enough. Seems like a difficult issue.

Thanks for the work you've put in on this project Gergely. It has been extremely helpful!

Jacob

RE: Export original 2017 Files

Gergely Csucs — Thu, 14 Oct 2021 15:36:38 GMT

[i]Originally posted by Jacob Bumgarner:[/i][quote]is there a way to propagate transformations in the VisuAlign program?
[/quote]There is none at the moment.
I can imagine a way, but haven't even tried it yet. The main issue is that in the general case the position and orientation of the actual tissue on a slide is a bit random. So if I just copy markers from one image to another directly, there may not be tissue at the given image position at all. But in fact the QuickNII-step does provide information about these irregularities, so in theory it may be possible to do the copy in "atlas-space" (which is uniform), and then transform it back into "image-space" (which has the randomness). But I don't know for sure if it would work, so I can't promise anything.

Best regards,
Gergely

RE: Export original 2017 Files

Jacob Bumgarner — Thu, 14 Oct 2021 14:51:23 GMT

Perfect - thanks for the tip Gergely.

I know that this is the wrong place to ask, but is there a way to propagate transformations in the VisuAlign program?

Jacob

RE: Export original 2017 Files

Gergely Csucs — Thu, 14 Oct 2021 10:27:46 GMT

Hi Jacob,

The simplest workaround is to download VisuAlign ( https://www.nitrc.org/projects/visualign/ ), as it saves both kind of overlay images. VisuAlign opens JSON files saved by QuickNII.

I hope this helps,
Gergely

Export original 2017 Files

Jacob Bumgarner — Wed, 13 Oct 2021 19:20:05 GMT

Hello,
Is there a way to export the Original 2017 mouse brain atlas and not just the Rainbow 2017 atlas?

Thanks,
Jacob

RE: Export slices with same resolution

Gergely Csucs — Mon, 13 Sep 2021 14:16:15 GMT

Hi Jacob,

QuickNII allows the user practically to find a suitable rectangle in the atlas which covers an entire image, with all of its squeezing and other possible distortions. Because of this, it's very unlikely that the identified rectangular atlas portions for a series of images are going to have the same dimensions. If the image series comes from block-face imaging, the chances are higher, but still not 100% sure. I didn't want to mislead users that there are tons of pixels/voxels in the atlas with infinite resolution, so the exported cuts have the actual dimensions in pixels what the identified 3D rectangles have in voxels. A practical detail is that this way the exported images are small.
There is some information about how image pixels and atlas voxels relate to each other here: https://www.nitrc.org/plugins/mwiki/index.php?title=quicknii:Image_coordinates
And while they haven't made yet into to Wiki, there are some practical ideas in neighboring topics, like how one can manually or programmatically overlay the resulting atlas cut on the actual image: https://www.nitrc.org/forum/forum.php?thread_id=12559&forum_id=9082 (manual) and https://www.nitrc.org/forum/forum.php?thread_id=12684&forum_id=9082 (Python)
For building volumes another direction is available though: creating a sparse NIfTI file from an aligned series, which can then be viewed together with the standard segmentation files in ITK Snap or similar tools. The example code for that is Java and it's available here: https://github.com/Tevemadar/QuickNII-extras/tree/master/Java

Best regards,
Gergely

RE: FileBuilder is not working properly

Gergely Csucs — Mon, 13 Sep 2021 12:31:53 GMT

Dear Ahn,

QuickNII itself supports PNG and JPEG images only, that's why FileBuilder doesn't allow creating series from TIFF images.
A possible ambiguity comes from that QuickNII works in screen-space, showing images in typically 1500*1000 pixels resolution, or only a little bit more. And QuickNII actually needs such images, the underlying runtime can't even load an image above 16 megapixels (say 4000x4000 pixels maximum). So most of the time a downscaling step is required (from original images coming from image acquisition equipment, to something screen-sized).
While the analytical tools, like Nutil, can and usually do work with much larger images, often several gigapixels in size, like 150000x100000 pixels, and such images are often easier to handle as TIFF, because it supports tiling for example.
Practically in our laboratory we maintain two sets of images for these workflows, one set of low-resolution images for QuickNII (and https://www.nitrc.org/projects/visualign/), and the actual original images for analysis.

Best regards,
Gergely

RE: Export slices with same resolution

Jacob Bumgarner — Fri, 10 Sep 2021 15:55:05 GMT

Hi Maja,
Has there been any consensus on whether this is a bug or if this is something that users need to manage on their own?

Thanks,
Jacob

RE: FileBuilder is not working properly

Maja Puchades — Fri, 03 Sep 2021 8:55:11 GMT

Dear Ahn,

Thank you for your question. I will follow up in our EBRAINS support system.

Best, Maja

RE: Export slices with same resolution

Maja Puchades — Fri, 03 Sep 2021 8:53:53 GMT

Dear Jacob,

Thank you for your question. I will create a ticket in our EBRAINS support system and follow up from there.

Best, Maja