fix(#103): replace mesh projection with direct atlas volume read#125
Open
ArielShadrac wants to merge 2 commits intobrainglobe:mainfrom
Open
fix(#103): replace mesh projection with direct atlas volume read#125ArielShadrac wants to merge 2 commits intobrainglobe:mainfrom
ArielShadrac wants to merge 2 commits intobrainglobe:mainfrom
Conversation
… Fixes ML-axis inversion and missing colours for parent regions.
for more information, see https://pre-commit.ci
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Add this suggestion to a batch that can be applied as a single commit.This suggestion is invalid because no changes were made to the code.Suggestions cannot be applied while the pull request is closed.Suggestions cannot be applied while viewing a subset of changes.Only one suggestion per line can be applied in a batch.Add this suggestion to a batch that can be applied as a single commit.Applying suggestions on deleted lines is not supported.You must change the existing code in this line in order to create a valid suggestion.Outdated suggestions cannot be applied.This suggestion has been applied or marked resolved.Suggestions cannot be applied from pending reviews.Suggestions cannot be applied on multi-line comments.Suggestions cannot be applied while the pull request is queued to merge.Suggestion cannot be applied right now. Please check back later.
Closes #103
Problem
The 2D frontal slice was showing only contours with no colours, and
the medio-lateral axis was inverted.
Before (bug #103)
After — correct colours and orientation
Code used to generate the render
```python import brainglobe_heatmap as bghdict1 = {
'mlf': 1.04, 'IO': 0.5, 'IP': 0.40, 'DCO': 0.88, 'VCO': 0.17,
'chpl': 0.14, 'IRN': 0.009, 'V4': 0.023, 'V4r': 0.11, 'PRP': 0.012,
'py': 0.38, 'MV': 0.097, 'SUV': 0.118, 'RO': 0.07, 'SPIV': 0.099,
'RPA': 0.467, 'MARN': 0.010, 'MY': 0.353, 'ICB': 0.056, 'SPVO': 0.036,
'das': 0.101, 'CB': 1.094, 'sctd': 1.318, 'NTS': 0.172, 'arb': 0.022,
'x': 0.112, 'sptV': 0.220, 'DN': 0.054, 'PARN': 0.009, 'rust': 0.042,
'sctv': 0.119, 'LING': 0.056, 'AMBd': 0.0, 'NOD': 0.419, 'PGRNd': 0.178,
'PGRNl': 0.025, 'FN': 0.016, 'PRM': 0.351, 'COPY': 0.267, 'PFL': 0.9,
'tspc': 0.020, 'GRN': 0.024, 'ANcr2': 0.280, 'icp': 0.096, 'VeCB': 0.053,
}
bgh.Heatmap(
dict1,
position=11500,
orientation="frontal",
thickness=100,
vmin=min(dict1.values()),
vmax=max(dict1.values()),
format="2D",
).show()