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Tomography reconstruction algos disabled #2295
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You need to mark your data as a Tilt series. Click Tomography -- Mark data as tilt series. Then those will be available. |
Unfortunately, tomopy's only supported installation method is through conda-forge, so we could not include it in the default packaging. If you want to try using the tomopy reconstruction algorithm, you'll need to first install tomviz from conda-forge ( |
thanks for the support @psavery . i installed tomviz using conda and also tomopy , however the reconstruction result is not 3D. can u please guide me what am doing wrong , as am new to tomviz current output using tomopy Gridrec reconstruction method however i was expecting output something like this : https://youtu.be/Bvj2gFvwjpU?si=2Acpcw6oC2mdQ52i&t=59 thanks a lot. |
I would try one of the non-tomopy reconstruction techniques to see if that is the issue. If you can share the data I might also be able to look into the issue. |
ok here is data sample : https://drive.google.com/file/d/1SC5RDziQ2qvWy6YClO52wby37WIQjm_C/view?usp=drive_link thanks |
Unfortunately, I do not think Tomviz can reconstruct your data. Tomviz expects the tilt axis to be perpendicular to the projection direction and does the reconstruction assuming rotation around only that one axis. You inclined your object perpendicular to the beam axis and then rotated it around the beam. Actually, the machine used to acquire the data (see your youtube video) rotates the source around the object. These are equivalent, but neither is compatible with Tomviz as far as Im aware. If you can reconstruct using a different software and then export it as a 3D volume then you can analyze the reconstruction. |
I Loaded my 60 tiff images capture via x ray scanner and then when i go to
Tomography
>Reconstruction
section i noticed all algo are disabled there ? so am wondering how to enable them like tomopy as am interested in reconstructing 3d mesh from my tiff stack. I even triedSample Data
menu to generate random particles but still tomography algos are disabled.To Reproduce
Steps to reproduce the behavior:
Tomography
>Reconstruction
Tomopy
methodExpected behavior
should be able to use and try various tomography reconstruction methods by default after installing the APP , as shown in the demo video.
Screenshots
![image](https://private-user-images.githubusercontent.com/12841788/327449404-32e1d952-6996-4273-ba29-ec715352d2d9.png?jwt=eyJhbGciOiJIUzI1NiIsInR5cCI6IkpXVCJ9.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.deiiuSIrZTlAEZRKPtN7Nxhy2lMENmJxdQ4bRgw_CzA)
My Data set screen shot
![image](https://private-user-images.githubusercontent.com/12841788/327450249-7bf1dd12-4613-4423-9b2b-db80593f7d64.png?jwt=eyJhbGciOiJIUzI1NiIsInR5cCI6IkpXVCJ9.eyJpc3MiOiJnaXRodWIuY29tIiwiYXVkIjoicmF3LmdpdGh1YnVzZXJjb250ZW50LmNvbSIsImtleSI6ImtleTUiLCJleHAiOjE3MjUxOTI2OTcsIm5iZiI6MTcyNTE5MjM5NywicGF0aCI6Ii8xMjg0MTc4OC8zMjc0NTAyNDktN2JmMWRkMTItNDYxMy00NDIzLTliMmItZGI4MDU5M2Y3ZDY0LnBuZz9YLUFtei1BbGdvcml0aG09QVdTNC1ITUFDLVNIQTI1NiZYLUFtei1DcmVkZW50aWFsPUFLSUFWQ09EWUxTQTUzUFFLNFpBJTJGMjAyNDA5MDElMkZ1cy1lYXN0LTElMkZzMyUyRmF3czRfcmVxdWVzdCZYLUFtei1EYXRlPTIwMjQwOTAxVDEyMDYzN1omWC1BbXotRXhwaXJlcz0zMDAmWC1BbXotU2lnbmF0dXJlPWQ4OWU3NzFkNmM2NTcwZWNhMTAwY2UyZjUyNGQ5ZjMyZjJhNDdiMGEwZjk3OTdhNWFjZTBmYjIxYTBhMDUwYmEmWC1BbXotU2lnbmVkSGVhZGVycz1ob3N0JmFjdG9yX2lkPTAma2V5X2lkPTAmcmVwb19pZD0wIn0.9tNYBBiTo0aAfgBPf_8D3LGrpBrBLh-6Z6mft99mzWk)
Desktop (please complete the following information):
Hardware (please complete the following information):
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