Which 3D formats are supported?

[dnke...@oakland.edu]

Hello. I'm using this tool for the 3D active mesh tool (which I believe has now merged into the active contours tool). I've tried opening obj, srf, and ply files, but all complain with a format not supported error. My question: what 3d file formats can open in Icy and more specifically: will all these formats work with the active contours (3D) tool? Thank you.

[Alexandre Dufour]

Hi “dnke...@oakland.edu”,

Icy relies essentially on the VTK library (and its eponym file format). This being said, even if you used the VTK format, there is (currently) no way to load it into Icy (I am working on this, including importers for other popular formats). The main issue is that mesh files (whichever format) don’t always have a spatial position that coincides with image coordinates (they are often centred on [0,0,0]), so I also have to implement some sort of mouse-interaction to move the mesh around (perhaps in 2D for a start).

Just to clarify: are you trying to import a mesh file into Icy to initialise the active contour tool and then segment some image data? 

Cheers

Alexandre

On 01 Oct 2015, at 21:57, dnke...@oakland.edu wrote:

Hello. I'm using this tool for the 3D active mesh tool (which I believe has now merged into the active contours tool). I've tried opening obj, srf, and ply files, but all complain with a format not supported error. My question: what 3d file formats can open in Icy and more specifically: will all these formats work with the active contours (3D) tool? Thank you.

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[David Keller]

Yes I'm trying to use the active contour tool to create a deformable
model that deforms around the 3D mesh. If there's no way to load 3D
meshes into icy, how do you use the 3D active contour tool? I've tried
opening vtk files, but they didn't work. Would you want console output
for the error? I have a project where I need to use deformable and
active meshes and this software seems to be the only open source
implementation. Thanks for the speedy reply!

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[Alexandre Dufour]

I’m not sure I follow what you want to achieve. 

The active contours plugin is an image segmentation tool, i.e. it takes an initial contour drawn inside an image and deforms it until the contour fits the image structures of interest, according to various energy terms (gradients, region homogeneity, etc.). The initial contour can be drawn manually (e.g. on 2D images) or generated by other plugins.

However I don’t see what you mean by “a deformable model that deforms around the 3D mesh”. The deformable model *is* the 3D mesh, and it deforms inside image data to fit pixel-defined structures. Could you be more specific on what you are trying to achieve?

As for the error message, again, you cannot *yet* load VTK files, because I haven’t published the importer yet.

Alexandre

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[David Keller]

My project involves having a 3D mesh and specifying a 3D ROI that will
inflate in the negative space of the 3D mesh. Also, how have the 3D
tools been tested in Icy if you cannot yet import 3D meshes? Thanks.

> https://groups.google.com/d/msgid/icy-software/679E5056-E183-45E3-8407-6CF98351317E%40pasteur.fr.

[Alexandre Dufour]

The way you describe it, it seems your project is not related to image analysis, so there might some confusion here.
The purpose of the active contours plugin is to create a 3D mesh from volumetric image data, not to load a 3D mesh from another software (what would we do with it if it’s already there??).
There is therefore no need to import 3D meshes, because we generate them from the image. They can be exported however (that’s the whole point!)

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[David Keller]

Is the volumetric image data a series of 2D images at known depths? So
the active mesh forms a 3D region from the list of 2D images? Thanks
for your help.

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[Alexandre Dufour]

Yes, the input data is a series of 2D images (sometimes called slices), usually at consecutive depths (in the case of biomedical imaging). And yes, the active mesh starts from an initial position in this volumetric data and creates a 3D mesh that deforms inside this volume.

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[David Keller]

What format would these 2D images need to be in? I'm wrestling with
the active contours plugin (which Icy says active mesh has merged
with) to demo the 3D active mesh implementation. By a series of images
do you mean a file such as gif which is an animated file that contains
multiple images? Or do you mean opening multiple jpg's? Thanks.

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[Alexandre Dufour]

Dear David,

I believe this conversation is not very productive due to misunderstanding and/or lack of clarity. This might be a reasonable moment to sit back, relax and for you to explain clearly what you wish to achieve with the plugin (or the software for that matter).

The icy software is meant to do image analysis, i.e. extract/quantify objects in images and videos, and is more specifically developed for 2D and 3D biological images.

If you are not familiar with any of these keywords, or if your project does not relate to any of these notions, there are high chances Icy won't be able to help. However if there *is* a relation, then a bit more detail from your side would be appreciated (alongside sample images to state your case).

Cheers
Alexandre

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[David Keller]

Hi Alexandre,

I've gotten a bit more clarity on my project. Its input is volumetric
data and an initial contour like you said. The initial contour deforms
within the volumetric data according to various energy terms like you
said.

What may be different is that the initial contour is a 3D mesh (vtk).
The output is the deformed 3D mesh (again vtk).

I don't yet have sample data to show you what I mean, but I believe
the 3D active mesh plugin implements what I'm trying to achieve.

Thanks,
David Keller

[Alexandre Dufour]

Hi David,

Thanks, that clarifies things a lot, and indeed that is something Icy (and the active contours plugin) can help you with.

What is currently missing is:
1. Importing a VTK mesh file in Icy
2. Exporting the deformed mesh as a VTK file

Although I already have a prototype for both operations, but there is a tricky aspect that needs to be sorted out first regarding the coordinate system. Your help will be very useful here: it would be great to know how you create the initial mesh and VTK file, (not just the software, but more importantly the coordinate system: are the vertices stored in pixels (relative to some dataset) or in metric units (with some arbitrary origin)? This is important to know in order to load the mesh at the proper coordinates in the dataset once inside Icy.

Once you start diving into this project and do have some sample files (image data and/or VTK file), feel free to post these files in this thread, that will help me finalise the plugin before publication online.

Cheers
Alexandre

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