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Custom refspace dimensions

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#47 2 comments 2 reactions 0 assignees View on GitHub

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Assessment

Difficulty
4/5
Estimated time
3-5 days
Newbie friendliness
35/100
Issue type
Feature
Clarity
Mostly clear
Activity status
Stale
Tech stack
python
Domain
data

Research direction

Start by locating the hardcoded refspace definition and the synchronization path that uses its micron bounds. Trace how coronal, transverse, and sagittal limits are applied, then verify that configurable limits prevent image regions from being cut off after synchronization.

Written by the indexing model from the issue text.

Description

We currently hardcode the respace to be (in microns). I guess because it is the canonical setup.

  refspace = (                                                                                                                                                                                                 
        ("coronal", (0, 13200),                                                                                                                                                                                                        
        ("transverse", (0, 8000),                                                                                                                                                                                                      
        ("sagittal",  (0, 11400),                                                                                                                                                                                                       
    )

The problem is that sometimes parts of images are cut off after synchronization. The cleanest solution is to just allow for dynamic resizing of the refspace. Something like.

  refspace = (                                                                                                                                                                                                 
        ("coronal", (c_max, c_min),                                                                                                                                                                                                        
        ("transverse", (t_min, t_max),                                                                                                                                                                                                      
        ("sagittal",  (s_min, s_max),                                                                                                                                                                                                       
    )
Dominant language
Python
Stars
17
Forks
8
No merged PRs in 30d

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