Ecosyste.ms: Issues

An open API service for providing issue and pull request metadata for open source projects.

GitHub / bluebrain/deep-atlas issues and pull requests

#78 - Update full_pipeline.py

Pull Request - State: open - Opened by dkeller9 11 months ago

#77 - Dimension incompatibility of NRRD files with ITK-snap

Pull Request - State: open - Opened by EmilieDel about 1 year ago

#76 - Dimension incompatibility of NRRD files with ITK-snap

Issue - State: open - Opened by Sebastien-PILUSO about 1 year ago - 1 comment

#75 - Add group id option to Dockerfile.

Pull Request - State: closed - Opened by drodarie over 1 year ago

#74 - Handle ITK Error (#73)

Pull Request - State: closed - Opened by EmilieDel almost 2 years ago

#72 - Output .npy files have shape (N, M, K, 3), instead of (N, M, K)

Issue - State: closed - Opened by HDictus about 2 years ago - 1 comment

#71 - GeneInterpolate not accepting border_predictions

Issue - State: open - Opened by HDictus about 2 years ago

#70 - Do not extrapolate when pair interpolation

Pull Request - State: closed - Opened by EmilieDel about 2 years ago

#69 - Nissl symmetry

Pull Request - State: closed - Opened by EmilieDel over 2 years ago

#68 - Considering a > 0 cutting angle

Issue - State: open - Opened by cveraszto over 2 years ago

#67 - Stop interpolation at the last slice

Issue - State: open - Opened by cveraszto over 2 years ago - 1 comment

#66 - Update README and Singularity image

Issue - State: open - Opened by EmilieDel over 2 years ago

#65 - Add information for interpolator checkpoints

Pull Request - State: closed - Opened by EmilieDel over 2 years ago

#64 - Add format option on the full pipeline

Pull Request - State: closed - Opened by EmilieDel over 2 years ago

#63 - Put every parameters optional

Pull Request - State: closed - Opened by EmilieDel over 2 years ago - 1 comment

#62 - Make CCFv3 optional

Pull Request - State: closed - Opened by EmilieDel over 2 years ago - 1 comment

#61 - Add default value when --help

Pull Request - State: closed - Opened by EmilieDel over 2 years ago

#60 - Display defaults in --help

Pull Request - State: closed - Opened by jankrepl over 2 years ago

#59 - Monitor interpolation memory usage when using GPUs

Issue - State: open - Opened by jankrepl over 2 years ago

#58 - Make sure Singularity does not load $HOME by default

Issue - State: open - Opened by jankrepl over 2 years ago

#57 - Put every parameters as optional for readibility

Issue - State: open - Opened by EmilieDel over 2 years ago

#56 - Print out defaults when `--help`

Issue - State: closed - Opened by jankrepl over 2 years ago

#55 - Put `CCFv3` path as optional path

Issue - State: closed - Opened by EmilieDel over 2 years ago

#54 - Feature/diogo issue 50

Pull Request - State: closed - Opened by drsantos89 over 2 years ago

#53 - Improve Dockerfile

Pull Request - State: closed - Opened by EmilieDel over 2 years ago

#52 - Problem when trying to download gene

Issue - State: closed - Opened by EmilieDel over 2 years ago - 2 comments

#51 - Better docker setup

Pull Request - State: closed - Opened by EmilieDel over 2 years ago - 1 comment

#50 - Docker image on Singularity

Issue - State: closed - Opened by FrancescoCasalegno over 2 years ago - 5 comments

#49 - Better docker setup

Issue - State: closed - Opened by FrancescoCasalegno over 2 years ago
Labels: documentation, enhancement

#48 - Turn resolution into a parameter (currently hardcoded)

Pull Request - State: open - Opened by EmilieDel over 2 years ago

#47 - Create dockerfile

Pull Request - State: closed - Opened by EmilieDel over 2 years ago - 2 comments

#46 - Update code with changes of `atlannot`

Pull Request - State: closed - Opened by EmilieDel over 2 years ago

#45 - Update code with changes of `atlannot`

Issue - State: closed - Opened by EmilieDel over 2 years ago

#44 - Handle gene slices outside of Nissl shape

Issue - State: open - Opened by EmilieDel over 2 years ago

#43 - Reintroduce remapping

Pull Request - State: closed - Opened by jankrepl over 2 years ago

#41 - Fix formatting logging message

Issue - State: open - Opened by jankrepl over 2 years ago

#40 - Add file handler for logging

Issue - State: open - Opened by jankrepl over 2 years ago

#39 - Various optimizations

Pull Request - State: closed - Opened by jankrepl over 2 years ago

#38 - Add verbose argument to the CLI

Issue - State: open - Opened by jankrepl over 2 years ago

#36 - Switch from `gene_id` to `experiment_id`

Pull Request - State: closed - Opened by EmilieDel over 2 years ago

#35 - Update section_numbers list when outside of nissl shape

Pull Request - State: closed - Opened by EmilieDel over 2 years ago - 2 comments

#34 - Handle slice number outside of the reference range

Issue - State: closed - Opened by jankrepl over 2 years ago - 1 comment

#33 - Improve README

Pull Request - State: closed - Opened by jankrepl over 2 years ago

#32 - Rename `gene_id` to something else

Issue - State: closed - Opened by jankrepl over 2 years ago - 1 comment

#31 - Add version specifiers for dependencies

Issue - State: closed - Opened by jankrepl over 2 years ago - 1 comment

#30 - Update README with the most important information

Issue - State: closed - Opened by jankrepl over 2 years ago - 2 comments

#29 - Drop remapping logic completely

Pull Request - State: closed - Opened by jankrepl over 2 years ago

#28 - Improve interpolation step

Pull Request - State: closed - Opened by EmilieDel over 2 years ago

#27 - Put `check_and_load` in utils.py and use it everywhere

Pull Request - State: closed - Opened by EmilieDel over 2 years ago - 1 comment

#26 - Add `--coordinate-sys` to the full-pipeline

Pull Request - State: closed - Opened by EmilieDel over 2 years ago

#25 - Add `--expression` flag to the full pipeline

Pull Request - State: closed - Opened by EmilieDel over 2 years ago

#24 - Profile the pipeline

Issue - State: open - Opened by jankrepl over 2 years ago

#23 - Expose `downsample_img` in the `full_pipeline`

Pull Request - State: closed - Opened by EmilieDel over 2 years ago

#22 - Mirror sagittal volumes

Pull Request - State: closed - Opened by EmilieDel over 2 years ago

#21 - Replace `gene_name` by `gene_id`

Pull Request - State: closed - Opened by EmilieDel over 2 years ago

#20 - Let the user choose the coordinate system

Issue - State: closed - Opened by jankrepl over 2 years ago

#19 - Turn resolution into a parameter (currently hardcoded)

Issue - State: open - Opened by jankrepl over 2 years ago

#18 - Make sure each stage (+ overall pipeline) reprodicible

Issue - State: open - Opened by jankrepl over 2 years ago - 1 comment

#17 - Add unit tests

Issue - State: open - Opened by jankrepl over 2 years ago

#16 - Mirror sagittal volumes

Issue - State: closed - Opened by jankrepl over 2 years ago

#15 - Think about removing the background

Issue - State: open - Opened by jankrepl over 2 years ago

#14 - Investigate why final interpolated volumes have dtype=float64

Issue - State: closed - Opened by jankrepl over 2 years ago - 1 comment

#13 - Improve pipeline management

Issue - State: open - Opened by jankrepl over 2 years ago

#12 - Introduce `use_expression` flag

Issue - State: closed - Opened by jankrepl over 2 years ago

#11 - Replace gene name with gene ID

Issue - State: closed - Opened by jankrepl over 2 years ago

#10 - Make sure remapping of labels only done once

Issue - State: closed - Opened by jankrepl over 2 years ago - 1 comment

#9 - Expose `downsample_img` to the `full_pipeline` CLI

Issue - State: closed - Opened by jankrepl over 2 years ago

#8 - Create Full Pipeline

Pull Request - State: closed - Opened by EmilieDel over 2 years ago

#7 - Add Acknowledgment + Copyright to `README.md`

Pull Request - State: closed - Opened by FrancescoCasalegno almost 3 years ago

#6 - Add banners

Pull Request - State: closed - Opened by EmilieDel almost 3 years ago

#5 - Add links to docs for all repositories

Pull Request - State: closed - Opened by Stannislav about 3 years ago

#4 - Add requirements.txt

Pull Request - State: closed - Opened by Stannislav about 3 years ago

#3 - Add Atlas Annotation and Atlas Interpolation to README

Pull Request - State: closed - Opened by Stannislav about 3 years ago

#2 - Add AUTHORS.txt

Pull Request - State: closed - Opened by Stannislav about 3 years ago - 1 comment

#1 - Add projects description

Pull Request - State: closed - Opened by EmilieDel about 3 years ago