Skip to content
This repository has been archived by the owner on Oct 6, 2021. It is now read-only.

Injection finder initial commit #11

Merged
merged 1 commit into from
Feb 4, 2020
Merged

Injection finder initial commit #11

merged 1 commit into from
Feb 4, 2020

Conversation

FedeClaudi
Copy link
Collaborator

Added code to extract injection site from raw images.

Usage:
Use neuro/injection_finder.py to extract injection site location.
This takes care of registering the data (neuro.registration.py), smoothing and thresholding the raw images and then extracting the surface of the injection site (marching cubes algorithm).
The result is saved as a .obj file that can be visualised in brain render.

This code is incomplete, the main functionality missing is to allow for the injection site to be reconstructed from the density of labelled cells around a target region.

Code doesn't conform to the contributing guidelines, but should be relatively easy to clean up.

@adamltyson adamltyson self-requested a review February 4, 2020 09:34
@adamltyson adamltyson self-assigned this Feb 4, 2020
@adamltyson adamltyson changed the base branch from master to injectionsite February 4, 2020 09:37
@adamltyson adamltyson merged commit 567c825 into SainsburyWellcomeCentre:injectionsite Feb 4, 2020
@adamltyson
Copy link
Member

Merging to edit on feature branch.

adamltyson added a commit that referenced this pull request Apr 16, 2020
@adamltyson @FedeClaudi @stephenlenzi
Refactor imports (#21)
ae09539 
* points to brainrender

* update testing

* refactor

* refactor

* badges

* notes

* initial inj finder commit (#11)

* formatting with black

* add .DS_store to gitignore

* typo

* update imports

* update imports

* deal with no obj path given

* error typo

* move utils too imlib

* remove amap imports

* optional logging to file

* tidy

* registration moved to imlib

* keep largest object

* reduce RAM usage

* remove unnecessary logging args

* adds lesion and track estimation and generic tools

* add missing dir support for cell export

* add missing dir support for cell export

* reduce mem requirements

* remove old code

* remove old code

* refactor scaling

* fix failing heatmap test

* update docs

* ensure output directory exists

* make pixel sizes mandatory

* make pixel sizes mandatory (#17)

* move functionality to imlib

* remove hard coded smoothing

* Refactor (#19)

* make pixel sizes mandatory

* move functionality to imlib

* remove hard coded smoothing

* update docs

* Injectionsite (#20)

* refactors code from SL to import from neuro and imlib only

* moves amap_vis to neuro and removes amap and cellfinder dependencies;

* format with black

* amap_vis

Co-authored-by: Federico Claudi <federicoclaudi@protonmail.com>
Co-authored-by: stephen <stephen.lenzi@gmail.com>
adamltyson added a commit that referenced this pull request Apr 17, 2020
@adamltyson @FedeClaudi @stephenlenzi
Add manual segmentation (#23)
5b98fc1 
* points to brainrender

* update testing

* refactor

* refactor

* badges

* notes

* initial inj finder commit (#11)

* formatting with black

* add .DS_store to gitignore

* typo

* update imports

* update imports

* deal with no obj path given

* error typo

* move utils too imlib

* remove amap imports

* optional logging to file

* tidy

* registration moved to imlib

* keep largest object

* reduce RAM usage

* remove unnecessary logging args

* adds lesion and track estimation and generic tools

* add missing dir support for cell export

* add missing dir support for cell export

* reduce mem requirements

* remove old code

* remove old code

* refactor scaling

* fix failing heatmap test

* update docs

* ensure output directory exists

* make pixel sizes mandatory

* make pixel sizes mandatory (#17)

* move functionality to imlib

* remove hard coded smoothing

* Refactor (#19)

* make pixel sizes mandatory

* move functionality to imlib

* remove hard coded smoothing

* update docs

* Injectionsite (#20)

* refactors code from SL to import from neuro and imlib only

* moves amap_vis to neuro and removes amap and cellfinder dependencies;

* format with black

* amap_vis

* bump

* remove cellfinder dependency

* cli entry point for fibre track segmentation

* refactor seg tools

* start manual seg

* remove hardocoding in manual region segmentation

* refactor paths

* bump

Co-authored-by: Federico Claudi <federicoclaudi@protonmail.com>
Co-authored-by: stephen <stephen.lenzi@gmail.com>
adamltyson added a commit that referenced this pull request Apr 20, 2020
@adamltyson @FedeClaudi @stephenlenzi
Support multiple regions (#26)
2e02dd2 
* points to brainrender

* update testing

* refactor

* refactor

* badges

* notes

* initial inj finder commit (#11)

* formatting with black

* add .DS_store to gitignore

* typo

* update imports

* update imports

* deal with no obj path given

* error typo

* move utils too imlib

* remove amap imports

* optional logging to file

* tidy

* registration moved to imlib

* keep largest object

* reduce RAM usage

* remove unnecessary logging args

* adds lesion and track estimation and generic tools

* add missing dir support for cell export

* add missing dir support for cell export

* reduce mem requirements

* remove old code

* remove old code

* refactor scaling

* fix failing heatmap test

* update docs

* ensure output directory exists

* make pixel sizes mandatory

* make pixel sizes mandatory (#17)

* move functionality to imlib

* remove hard coded smoothing

* Refactor (#19)

* make pixel sizes mandatory

* move functionality to imlib

* remove hard coded smoothing

* update docs

* Injectionsite (#20)

* refactors code from SL to import from neuro and imlib only

* moves amap_vis to neuro and removes amap and cellfinder dependencies;

* format with black

* amap_vis

* bump

* remove cellfinder dependency

* cli entry point for fibre track segmentation

* refactor seg tools

* start manual seg

* remove hardocoding in manual region segmentation

* refactor paths

* bump

* update docs

* update docs

* update docs

* update docs

* support multiple objects

* color objects

* bump

* update reqs

Co-authored-by: Federico Claudi <federicoclaudi@protonmail.com>
Co-authored-by: stephen <stephen.lenzi@gmail.com>
adamltyson added a commit that referenced this pull request Apr 22, 2020
@adamltyson @FedeClaudi @stephenlenzi
bump (#27)
33573d5 
* points to brainrender

* update testing

* refactor

* refactor

* badges

* notes

* initial inj finder commit (#11)

* formatting with black

* add .DS_store to gitignore

* typo

* update imports

* update imports

* deal with no obj path given

* error typo

* move utils too imlib

* remove amap imports

* optional logging to file

* tidy

* registration moved to imlib

* keep largest object

* reduce RAM usage

* remove unnecessary logging args

* adds lesion and track estimation and generic tools

* add missing dir support for cell export

* add missing dir support for cell export

* reduce mem requirements

* remove old code

* remove old code

* refactor scaling

* fix failing heatmap test

* update docs

* ensure output directory exists

* make pixel sizes mandatory

* make pixel sizes mandatory (#17)

* move functionality to imlib

* remove hard coded smoothing

* Refactor (#19)

* make pixel sizes mandatory

* move functionality to imlib

* remove hard coded smoothing

* update docs

* Injectionsite (#20)

* refactors code from SL to import from neuro and imlib only

* moves amap_vis to neuro and removes amap and cellfinder dependencies;

* format with black

* amap_vis

* bump

* remove cellfinder dependency

* cli entry point for fibre track segmentation

* refactor seg tools

* start manual seg

* remove hardocoding in manual region segmentation

* refactor paths

* bump

* update docs

* update docs

* update docs

* update docs

* support multiple objects

* color objects

* bump

* update reqs

* improve rendering of flat objects

* bump

* prevent saving unnecessary common volume

* allow ROIs to be edited

* label regions

* bump

* bump

Co-authored-by: Federico Claudi <federicoclaudi@protonmail.com>
Co-authored-by: stephen <stephen.lenzi@gmail.com>
Sign up for free to subscribe to this conversation on GitHub. Already have an account? Sign in.
Reviewers

@adamltyson adamltyson Awaiting requested review from adamltyson

Assignees

@adamltyson adamltyson

Labels
None yet
Projects
None yet
Milestone
No milestone
Development

Successfully merging this pull request may close these issues.
2 participants
@FedeClaudi @adamltyson