Comments (4)
This is relevant especially for handling template matching results, since they come out rescaled from 0 to 1. We need to figure out:
- when we can retrieve the scale (is it present in the starfile, or can we only retrieve it from the images?)
- where we want to store this information (probably some attribute in the particle block)
- how to cleanly deal with this at napari level
from blik.
Definitely, a combination of this and #50 all existing under the same '.star' file are why I thought having one all encompassing peeper was maybe a lofty goal.
Currently we can retrieve scale from RELION 3.1 star files, user input and the image files themselves, none of which are guaranteed to be correct
- dynamo doesn't write pixel sizes into the headers of volumes as standard
- RELION <3.1 STAR files don't contain pixel size info, some (but not all) of them contain magnification and detector pixel size info
- Warp STAR files from template matching have no info about the volume they come from (to infer position) or the pixel size of that volume
Hard problem, definitely needs to be handled with care.
One solution is just to always ask for a pixel size, although that's quickly annoying if you know that the information is available in the files you provided
We could also explicitly handle each case and provide warnings when we know things are likely wrong?
from blik.
I'm gonna think about it a bit. I think it should be possible to guess some things, fetch others from files, and as last resort ask for what's missing.
from blik.
Closed by #69 .
from blik.
Related Issues (20)
- Import times are SLOW HOT 3
- Documentation
- Use dask HOT 5
- failed reading of star file HOT 1
- Images HOT 4
- Dependency issues HOT 2
- Failed to load mrc HOT 9
- saving files should add extension if needed
- saving star file does not save pixel size correctly HOT 1
- issue with star file reading? HOT 7
- reducing coordinate opacity makes black dots on the image layer HOT 12
- Generating the same particle twice overrides the existing layer but with broken orientations HOT 2
- Minor issue: expected MRC file extension HOT 1
- Suggestion: show tomograms in the same orientation as IMOD HOT 3
- out of slice fading of point and orientation layer HOT 2
- colouring points by data attribute HOT 4
- install error using Napari GUI HOT 7
- gaussian filter has no "Run" button HOT 2
- I can't open a simple star HOT 1
- Update tutorial
Recommend Projects
-
React
A declarative, efficient, and flexible JavaScript library for building user interfaces.
-
Vue.js
🖖 Vue.js is a progressive, incrementally-adoptable JavaScript framework for building UI on the web.
-
Typescript
TypeScript is a superset of JavaScript that compiles to clean JavaScript output.
-
TensorFlow
An Open Source Machine Learning Framework for Everyone
-
Django
The Web framework for perfectionists with deadlines.
-
Laravel
A PHP framework for web artisans
-
D3
Bring data to life with SVG, Canvas and HTML. 📊📈🎉
-
Recommend Topics
-
javascript
JavaScript (JS) is a lightweight interpreted programming language with first-class functions.
-
web
Some thing interesting about web. New door for the world.
-
server
A server is a program made to process requests and deliver data to clients.
-
Machine learning
Machine learning is a way of modeling and interpreting data that allows a piece of software to respond intelligently.
-
Visualization
Some thing interesting about visualization, use data art
-
Game
Some thing interesting about game, make everyone happy.
Recommend Org
-
Facebook
We are working to build community through open source technology. NB: members must have two-factor auth.
-
Microsoft
Open source projects and samples from Microsoft.
-
Google
Google ❤️ Open Source for everyone.
-
Alibaba
Alibaba Open Source for everyone
-
D3
Data-Driven Documents codes.
-
Tencent
China tencent open source team.
from blik.