3D reconstruction from 2D - image-processing

I've 2D slices of a 3D micro CT image. The image stack is available in .tif format.
In the original study, 3D reconstruction has been performed using Imaris software. I'd like
to reproduce the results presented in the original paper. However, I don't have a license for Imaris.
I tried to use 3D Slicer which is an open source software. I could load the images, but couldn't generate the 3D volume. I can provide further details if someone has worked on this tool.
I intend to create a 3D volume from the segmented images and filter the skeleton based on its thickness.
Post this, I'd like to delete some branches of the skeleton. For instance, if there are 500 branches, I would like to reduce it by an order of magnitude by deleting branches (selecting a particular region of interest). I'm a beginner in this field and I'm not sure which tool can be used.
Any suggestions on how to proceed will be really helpful.

Related

Panorama of cylindric objects

I want to get the panorama view of cylindrical objects without using special cameras.
The idea was to get a lot of images from different views, cut the center and join these centers together. But I got bad results.
May be somebody knows the best solution for this purpose? May be it's better recognize from video?
Hugin is a great configurable and agile free cross-platform software to stitch panoramic images. You can definitely use it for your task.
If you want to create your own tool for that purpose, you may find useful to read about Hugin's toolchain workflow to know what steps may be needed to achieve nice results.
A possible work flow may be
Take images.
Correct projection depending on lense parameters.
Find and verify control points on image pairs (possible algorithms: SIFT, SURF).
Geometric optimisation (shift, 3D rotation, etc).
Photometric optimisation (exposure values, vignetting, white balance).
Stitch and blend output (cut the centers and join them smoothly together).
You may skip some steps depending on your image capturing conditions. The more similar images are (same camera and cylinder positions, same lighting, etc.) the less image correction you will need.

Computer Vision: "Inverse" Structure From Motion

Note: I am not asking for code just the name of some algorithms I can research
Problem
I'm trying to do a 3D reconstruction from multiple images where the subject is rotating.
I don't have a lot of experience in the CV field and my mathematics is not particularly good so I am reliant on either simply worded papers or existing libraries/tools.
Where I'm At
I have been researching and testing using Structure from Motion (with VisualSFM) to generate a 3d point cloud and Multi View Stereo (with CMPMVS) to reconstruct the scene.
Obviously these algorithms are designed to process images where the camera (or cameras) moves and the scene is stationary so the reconstructions fail for a number of reasons.
Example: I've been working with short videos of a person rotating around a marker on the floor, see below. I've tried removing the background but this seems to make it harder for SfM to build pairs, probably because of the lack of intformation.
Question
Does anyone know the name of an algorithm/pipeline that will be able to reconstruct a series of images with a static background and a rotating object?
Or is it not possible to do a 3d reconstruction in this way?

Wikitude/AR SDK's to Pick out objects in 3d space

Im looking at integrating an AR Kit into our iOS App so we can use the camera to scan a room or field of view for objects. Above is an example of what i mean, if you were to bring up the camera it would highlight the separate objects in the room and allow them to be clicked and "added" into the system.
Does anyone know if this is achievable with the current AR kits or anything else out there? It all seems to be the fact that objects that you are looking for have to be pre-defined and loaded into a database so the app can find them. Im hoping it should be able to pick out the objects realtime. It doesnt need to actually know any details on the actual object just so that can be pulled off the base scenary.
Any ideas?
OpenCV library (iOS) contains many algorithms to compare different image blobs. If you want to match some simple template to find objects then try Viola & Jones algorithm and so called Haar cascades. OpenCV has trained collection of templates in XML files for detecting faces for example. OpenCV contains utility for training thus you are able to generate cascades for other kinds of objects.
Some example projects:
https://github.com/alexmac/alcexamples/blob/master/OpenCV-2.4.2/doc/user_guide/ug_traincascade.rst Cascade Classifier Training
https://github.com/lukagabric/iOS-OpenCV Example code for detecting Colors and Circle shapes
https://github.com/BloodAxe/OpenCV-Tutorial Feature Detection (SURF, ORB, FREAK)
https://github.com/foundry/OpenCVSquaresSL Square Detection using Pyramid scaling, Canny, contours, contour simpification

opencv matching edge images

I am working on the project and part of it is to recognize objects recorded on camera. So to be more specific:
I am using OpenCV
I have correctly setup camera and am able to retrieve pictures from it
I have compiled and experimented with number of demos from OpenCV
I need a scale- AND rotation- invariant algorithm for detection
Pictures of original objects are ONLY available as edge-images
All feature detection/extraction/matching algorithms I have seen so far are working reasonably well with gray-scale images (like photos), however due to my project specs I need to work with edge images (kinda like output of canny edge detector) which are typically BW and contain only edges found within the image. In this case the performance of algorithms I was trying to use (SURF, SIFT, MSER, etc) decreases dramatically.
So the actual question is: Has anyone come across algorithm that would be specific for matching edge images or is there a certain setup that can improve performance of SIFR/SURF/? in order to work well with that kind of input.
I would appretiate any advice or links to any relevant resources
PS: this is my first question of stackoverflow
Edge images have a problem: The information they contain about the objects of interest is very, very scarce.
So, a general algorithm to classify edge images is probably not to be found. However, if your images are simple, clear and specific, you can employ a number of techniques to classify them. Among them: find contours, and select by shape, area, positioning, tracking.
A good list of shape information (from Matlab help site) includes:
'Area'
'EulerNumber'
'Orientation'
'BoundingBox'
'Extent'
'Perimeter'
'Centroid'
'Extrema'
'PixelIdxList'
'ConvexArea'
'FilledArea'
'PixelList'
'ConvexHull'
'FilledImage'
'Solidity'
'ConvexImage'
'Image'
'SubarrayIdx'
'Eccentricity'
'MajorAxisLength'
'EquivDiameter'
'MinorAxisLength'
An important condition to use shapes in your algorithm is to be able to select them individually. Shape analysis is very sensitive to noise, overlap, etc
Update
I found a paper that may be interesting in this context - it is an object classifier that only uses shape information, and it can be applied on Canny images - it sounds like it's your solution
http://www.vision.ee.ethz.ch/publications/papers/articles/eth_biwi_00664.pdf

3D reconstruction -- How to create 3D model from 2D image?

If I take a picture with a camera, so I know the distance from the camera to the object, such as a scale model of a house, I would like to turn this into a 3D model that I can maneuver around so I can comment on different parts of the house.
If I sit down and think about taking more than one picture, labeling direction, and distance, I should be able to figure out how to do this, but, I thought I would ask if someone has some paper that may help explain more.
What language you explain in doesn't matter, as I am looking for the best approach.
Right now I am considering showing the house, then the user can put in some assistance for height, such as distance from the camera to the top of that part of the model, and given enough of this it would be possible to start calculating heights for the rest, especially if there is a top-down image, then pictures from angles on the four sides, to calculate relative heights.
Then I expect that parts will also need to differ in color to help separate out the various parts of the model.
As mentioned, the problem is very hard and is often also referred to as multi-view object reconstruction. It is usually approached by solving the stereo-view reconstruction problem for each pair of consecutive images.
Performing stereo reconstruction requires that pairs of images are taken that have a good amount of visible overlap of physical points. You need to find corresponding points such that you can then use triangulation to find the 3D co-ordinates of the points.
Epipolar geometry
Stereo reconstruction is usually done by first calibrating your camera setup so you can rectify your images using the theory of epipolar geometry. This simplifies finding corresponding points as well as the final triangulation calculations.
If you have:
the intrinsic camera parameters (requiring camera calibration),
the camera's position and rotation (it's extrinsic parameters), and
8 or more physical points with matching known positions in two photos (when using the eight-point algorithm)
you can calculate the fundamental and essential matrices using only matrix theory and use these to rectify your images. This requires some theory about co-ordinate projections with homogeneous co-ordinates and also knowledge of the pinhole camera model and camera matrix.
If you want a method that doesn't need the camera parameters and works for unknown camera set-ups you should probably look into methods for uncalibrated stereo reconstruction.
Correspondence problem
Finding corresponding points is the tricky part that requires you to look for points of the same brightness or colour, or to use texture patterns or some other features to identify the same points in pairs of images. Techniques for this either work locally by looking for a best match in a small region around each point, or globally by considering the image as a whole.
If you already have the fundamental matrix, it will allow you to rectify the images such that corresponding points in two images will be constrained to a line (in theory). This helps you to use faster local techniques.
There is currently still no ideal technique to solve the correspondence problem, but possible approaches could fall in these categories:
Manual selection: have a person hand-select matching points.
Custom markers: place markers or use specific patterns/colours that you can easily identify.
Sum of squared differences: take a region around a point and find the closest whole matching region in the other image.
Graph cuts: a global optimisation technique based on optimisation using graph theory.
For specific implementations you can use Google Scholar to search through the current literature. Here is one highly cited paper comparing various techniques:
A Taxonomy and Evaluation of Dense Two-Frame Stereo Correspondence Algorithms.
Multi-view reconstruction
Once you have the corresponding points, you can then use epipolar geometry theory for the triangulation calculations to find the 3D co-ordinates of the points.
This whole stereo reconstruction would then be repeated for each pair of consecutive images (implying that you need an order to the images or at least knowledge of which images have many overlapping points). For each pair you would calculate a different fundamental matrix.
Of course, due to noise or inaccuracies at each of these steps you might want to consider how to solve the problem in a more global manner. For instance, if you have a series of images that are taken around an object and form a loop, this provides extra constraints that can be used to improve the accuracy of earlier steps using something like bundle adjustment.
As you can see, both stereo and multi-view reconstruction are far from solved problems and are still actively researched. The less you want to do in an automated manner the more well-defined the problem becomes, but even in these cases quite a bit of theory is required to get started.
Alternatives
If it's within the constraints of what you want to do, I would recommend considering dedicated hardware sensors (such as the XBox's Kinect) instead of only using normal cameras. These sensors use structured light, time-of-flight or some other range imaging technique to generate a depth image which they can also combine with colour data from their own cameras. They practically solve the single-view reconstruction problem for you and often include libraries and tools for stitching/combining multiple views.
Epipolar geometry references
My knowledge is actually quite thin on most of the theory, so the best I can do is to further provide you with some references that are hopefully useful (in order of relevance):
I found a PDF chapter on Multiple View Geometry that contains most of the critical theory. In fact the textbook Multiple View Geometry in Computer Vision should also be quite useful (sample chapters available here).
Here's a page describing a project on uncalibrated stereo reconstruction that seems to include some source code that could be useful. They find matching points in an automated manner using one of many feature detection techniques. If you want this part of the process to be automated as well, then SIFT feature detection is commonly considered to be an excellent non-real-time technique (since it's quite slow).
A paper about Scene Reconstruction from Multiple Uncalibrated Views.
A slideshow on Methods for 3D Reconstruction from Multiple Images (it has some more references below it's slides towards the end).
A paper comparing different multi-view stereo reconstruction algorithms can be found here. It limits itself to algorithms that "reconstruct dense object models from calibrated views".
Here's a paper that goes into lots of detail for the case that you have stereo cameras that take multiple images: Towards robust metric reconstruction
via a dynamic uncalibrated stereo head. They then find methods to self-calibrate the cameras.
I'm not sure how helpful all of this is, but hopefully it includes enough useful terminology and references to find further resources.
Research has made significant progress and these days it is possible to obtain pretty good-looking 3D shapes from 2D images. For instance, in our recent research work titled "Synthesizing 3D Shapes via Modeling Multi-View Depth Maps and Silhouettes With Deep Generative Networks" took a big step in solving the problem of obtaining 3D shapes from 2D images. In our work, we show that you can not only go from 2D to 3D directly and get a good, approximate 3D reconstruction but you can also learn a distribution of 3D shapes in an efficient manner and generate/synthesize 3D shapes. Below is an image of our work showing that we are able to do 3D reconstruction even from a single silhouette or depth map (on the left). The ground-truth 3D shapes are shown on the right.
The approach we took has some contributions related to cognitive science or the way the brain works: the model we built shares parameters for all shape categories instead of being specific to only one category. Also, it obtains consistent representations and takes the uncertainty of the input view into account when producing a 3D shape as output. Therefore, it is able to naturally give meaningful results even for very ambiguous inputs. If you look at the citation to our paper you can see even more progress just in terms of going from 2D images to 3D shapes.
This problem is known as Photogrammetry.
Google will supply you with endless references, just be aware that if you want to roll your own, it's a very hard problem.
Check out The Deadalus Project, althought that website does not contain a gallery with illustrative information about the solution, it post several papers and info about the working method.
I watched a lecture from one of the main researchers of the project (Roger Hubbold), and the image results are quite amazing! Althought is a complex and long problem. It has a lot of tricky details to take into account to get an approximation of the 3d data, take for example the 3d information from wall surfaces, for which the heuristic to work is as follows: Take a photo with normal illumination of the scene, and then retake the picture in same position with full flash active, then substract both images and divide the result by a pre-taken flash calibration image, apply a box filter to this new result and then post-process to estimate depth values, the whole process is explained in detail in this paper (which is also posted/referenced in the project website)
Google Sketchup (free) has a photo matching tool that allows you to take a photograph and match its perspective for easy modeling.
EDIT: It appears that you're interested in developing your own solution. I thought you were trying to obtain a 3D model of an image in a single instance. If this answer isn't helpful, I apologize.
Hope this helps if you are trying to construct 3d volume from 2d stack of images !! You can use open source tool such as ImageJ Fiji which comes with 3d viewer plugin..
https://quppler.com/creating-a-classifier-using-image-j-fiji-for-3d-volume-data-preparation-from-stack-of-images/

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