Scikit-Image: turning stack scans into a 3d image
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I'm currently doing a bit of research on how to access 3d data using scikit-image specifically. And I have a stack of jpg image files that I want to turn into a 3d image.
I've been able to convert these images into 3d form using Fiji (ImageJ), and I'm wondering if I can do the same (or something similar) in scikit-image. I've been looking at the introductory examples in the scikit-image but I can't seem to find anything similar to what I'm looking for. Below is an image of what I'm hoping to achieve using scikit-image:
If anyone has any suggestions on how to use scikit-image to re-create 2d stack image scans into 3d images that would be great. Thanks in advance.
python scikit-learn
edited Nov 20 '18 at 0:56
Richard
28.1k19110174
asked Nov 16 '18 at 21:53
Jvn KicJvn Kic
63
add a comment |
I'm currently doing a bit of research on how to access 3d data using scikit-image specifically. And I have a stack of jpg image files that I want to turn into a 3d image.
I've been able to convert these images into 3d form using Fiji (ImageJ), and I'm wondering if I can do the same (or something similar) in scikit-image. I've been looking at the introductory examples in the scikit-image but I can't seem to find anything similar to what I'm looking for. Below is an image of what I'm hoping to achieve using scikit-image:
If anyone has any suggestions on how to use scikit-image to re-create 2d stack image scans into 3d images that would be great. Thanks in advance.
python scikit-learn
edited Nov 20 '18 at 0:56
Richard
28.1k19110174
asked Nov 16 '18 at 21:53
Jvn KicJvn Kic
63
Is it possible for you to provide a link to your slices or an analogous image set?
– Richard
Nov 20 '18 at 0:57
I got my image slices (for the specific image above) from MorphoSource: morphosource.org/Detail/MediaDetail/Show/media_id/16076 . You can create a free account and download the files from there. And perhaps to provide a little bit of reference, my research is primarily focused on how to extract and access 3D data. I'm not too familiar with scikit-image but my hope is to provide a manual of sorts to help others reproduce/access/extract 3D data like those from MorphoSource.
– Jvn Kic
Nov 27 '18 at 6:10
add a comment |
I'm currently doing a bit of research on how to access 3d data using scikit-image specifically. And I have a stack of jpg image files that I want to turn into a 3d image.
I've been able to convert these images into 3d form using Fiji (ImageJ), and I'm wondering if I can do the same (or something similar) in scikit-image. I've been looking at the introductory examples in the scikit-image but I can't seem to find anything similar to what I'm looking for. Below is an image of what I'm hoping to achieve using scikit-image:
If anyone has any suggestions on how to use scikit-image to re-create 2d stack image scans into 3d images that would be great. Thanks in advance.
python scikit-learn
edited Nov 20 '18 at 0:56
Richard
28.1k19110174
asked Nov 16 '18 at 21:53
Jvn KicJvn Kic
63
I'm currently doing a bit of research on how to access 3d data using scikit-image specifically. And I have a stack of jpg image files that I want to turn into a 3d image.
I've been able to convert these images into 3d form using Fiji (ImageJ), and I'm wondering if I can do the same (or something similar) in scikit-image. I've been looking at the introductory examples in the scikit-image but I can't seem to find anything similar to what I'm looking for. Below is an image of what I'm hoping to achieve using scikit-image:
If anyone has any suggestions on how to use scikit-image to re-create 2d stack image scans into 3d images that would be great. Thanks in advance.
python scikit-learn
python scikit-learn
edited Nov 20 '18 at 0:56
Richard
28.1k19110174
asked Nov 16 '18 at 21:53
Jvn KicJvn Kic
63
edited Nov 20 '18 at 0:56
Richard
28.1k19110174
asked Nov 16 '18 at 21:53
Jvn KicJvn Kic
63
edited Nov 20 '18 at 0:56
Richard
28.1k19110174
edited Nov 20 '18 at 0:56
Richard
28.1k19110174
edited Nov 20 '18 at 0:56
Richard
28.1k19110174
28.1k19110174
asked Nov 16 '18 at 21:53
Jvn KicJvn Kic
63
asked Nov 16 '18 at 21:53
Jvn KicJvn Kic
63
asked Nov 16 '18 at 21:53
Jvn KicJvn Kic
63
63
Is it possible for you to provide a link to your slices or an analogous image set?
– Richard
Nov 20 '18 at 0:57
I got my image slices (for the specific image above) from MorphoSource: morphosource.org/Detail/MediaDetail/Show/media_id/16076 . You can create a free account and download the files from there. And perhaps to provide a little bit of reference, my research is primarily focused on how to extract and access 3D data. I'm not too familiar with scikit-image but my hope is to provide a manual of sorts to help others reproduce/access/extract 3D data like those from MorphoSource.
– Jvn Kic
Nov 27 '18 at 6:10
add a comment |
Is it possible for you to provide a link to your slices or an analogous image set?
– Richard
Nov 20 '18 at 0:57
I got my image slices (for the specific image above) from MorphoSource: morphosource.org/Detail/MediaDetail/Show/media_id/16076 . You can create a free account and download the files from there. And perhaps to provide a little bit of reference, my research is primarily focused on how to extract and access 3D data. I'm not too familiar with scikit-image but my hope is to provide a manual of sorts to help others reproduce/access/extract 3D data like those from MorphoSource.
– Jvn Kic
Nov 27 '18 at 6:10
Is it possible for you to provide a link to your slices or an analogous image set?
– Richard
Nov 20 '18 at 0:57
Is it possible for you to provide a link to your slices or an analogous image set?
– Richard
Nov 20 '18 at 0:57
I got my image slices (for the specific image above) from MorphoSource: morphosource.org/Detail/MediaDetail/Show/media_id/16076 . You can create a free account and download the files from there. And perhaps to provide a little bit of reference, my research is primarily focused on how to extract and access 3D data. I'm not too familiar with scikit-image but my hope is to provide a manual of sorts to help others reproduce/access/extract 3D data like those from MorphoSource.
– Jvn Kic
Nov 27 '18 at 6:10
I got my image slices (for the specific image above) from MorphoSource: morphosource.org/Detail/MediaDetail/Show/media_id/16076 . You can create a free account and download the files from there. And perhaps to provide a little bit of reference, my research is primarily focused on how to extract and access 3D data. I'm not too familiar with scikit-image but my hope is to provide a manual of sorts to help others reproduce/access/extract 3D data like those from MorphoSource.
– Jvn Kic
Nov 27 '18 at 6:10
add a comment |
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Is it possible for you to provide a link to your slices or an analogous image set?
– Richard
Nov 20 '18 at 0:57
I got my image slices (for the specific image above) from MorphoSource: morphosource.org/Detail/MediaDetail/Show/media_id/16076 . You can create a free account and download the files from there. And perhaps to provide a little bit of reference, my research is primarily focused on how to extract and access 3D data. I'm not too familiar with scikit-image but my hope is to provide a manual of sorts to help others reproduce/access/extract 3D data like those from MorphoSource.
– Jvn Kic
Nov 27 '18 at 6:10