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Binning nuclear labels #222

Merged
merged 3 commits into from
Sep 15, 2020
Merged

Binning nuclear labels #222

merged 3 commits into from
Sep 15, 2020

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ngreenwald
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If you haven't already, please read through our contributing guidelines before opening your PR

What is the purpose of this PR?
Currently, when we match nuclei to cells, we don't require that the nucleus be smaller than the cell. If the nuclear segmentation has errors, this can result in non-biological readouts.

This PR adds the option to separate out nuclei that are larger than a cell, and relabel the portion that falls within a cell, to remove this issue

How did you implement your changes
Added a function that takes a nuclear mask and a cell mask, and relabels any nuclei that have pixels outside of the boundaries of the corresponding cell they map to.

Remaining issues

Still need to integrate this into the overall segmentation pipeline

ackagel
ackagel reviewed Sep 15, 2020
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Looks good; mostly just a clarification question.

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alex-l-kong
alex-l-kong previously approved these changes Sep 15, 2020
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Looks good to me.

alex-l-kong
alex-l-kong approved these changes Sep 15, 2020
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Looks mighty fine.

ackagel
ackagel approved these changes Sep 15, 2020
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cool cool cool

@ngreenwald ngreenwald merged commit f1bafdb into master Sep 15, 2020
@ngreenwald ngreenwald deleted the modify_nuc_labels branch September 15, 2020 21:46
@ngreenwald ngreenwald mentioned this pull request Sep 15, 2020
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alex-l-kong pushed a commit that referenced this pull request Jan 14, 2021
@ngreenwald
Binning nuclear labels (#222)
22a5afa 
* first pass

* fix formatting
y2kbugger pushed a commit that referenced this pull request Jul 29, 2021
@ngreenwald
Binning nuclear labels (#222)
5140b37 
* first pass

* fix formatting
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@ackagel ackagel ackagel approved these changes

@alex-l-kong alex-l-kong alex-l-kong approved these changes

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3 participants
@ngreenwald @alex-l-kong @ackagel