nerc-ceh/plankton_ml issues and pull requests

#64 - Label Studio ML backend

Issue - State: open - Opened by metazool 22 days ago

#63 - Pipeline filenames - bugfix

Pull Request - State: closed - Opened by metazool 29 days ago

#62 - Reynolds values

Issue - State: open - Opened by metazool about 1 month ago

#62 - Reynolds values

Issue - State: open - Opened by metazool about 1 month ago

#61 - Use directory names to derive pipeline experiment names

Pull Request - State: closed - Opened by metazool about 2 months ago

#61 - Use directory names to derive pipeline experiment names

Pull Request - State: closed - Opened by metazool about 2 months ago

#60 - Naming files based on directory naming conventions

Issue - State: closed - Opened by metazool about 2 months ago - 1 comment

#60 - Naming files based on directory naming conventions

Issue - State: closed - Opened by metazool about 2 months ago - 1 comment

#59 - Quick visualisation of classification results

Pull Request - State: closed - Opened by metazool about 2 months ago

#59 - Quick visualisation of classification results

Pull Request - State: closed - Opened by metazool about 2 months ago

#58 - Fastapi model serving

Pull Request - State: closed - Opened by metazool 2 months ago - 1 comment

#58 - Fastapi model serving

Pull Request - State: closed - Opened by metazool 2 months ago - 1 comment

#57 - Run this on Phenocam imagery

Issue - State: closed - Opened by metazool 2 months ago - 5 comments

#57 - Run this on Phenocam imagery

Issue - State: closed - Opened by metazool 2 months ago - 5 comments

#56 - Support for different vector stores

Pull Request - State: closed - Opened by metazool 2 months ago - 1 comment

#55 - Flow cytometer data transfer

Issue - State: open - Opened by metazool 3 months ago

#54 - Workflow docs - diagram and draft presentation

Pull Request - State: closed - Opened by metazool 3 months ago

#54 - Workflow docs - diagram and draft presentation

Pull Request - State: closed - Opened by metazool 3 months ago

#53 - Fastapi model serving

Pull Request - State: closed - Opened by metazool 3 months ago - 1 comment

#52 - FastAPI model serving

Issue - State: open - Opened by metazool 3 months ago - 1 comment

#52 - FastAPI model serving

Issue - State: closed - Opened by metazool 3 months ago - 2 comments

#51 - Tweaks and fixes for the image upload pipeline

Pull Request - State: closed - Opened by metazool 3 months ago

#51 - Tweaks and fixes for the image upload pipeline

Pull Request - State: closed - Opened by metazool 3 months ago

#50 - Object store docs

Pull Request - State: closed - Opened by metazool 3 months ago

#49 - Luigi pipeline related changes

Pull Request - State: closed - Opened by metazool 3 months ago

#49 - Luigi pipeline related changes

Pull Request - State: closed - Opened by metazool 3 months ago

#48 - Flow cytometer data handling

Pull Request - State: closed - Opened by metazool 3 months ago

#48 - Flow cytometer data handling

Pull Request - State: closed - Opened by metazool 3 months ago

#47 - Deployment of image processing, ideally somewhere maintained by others!

Issue - State: open - Opened by metazool 3 months ago - 5 comments

#47 - Deployment of image processing, ideally somewhere maintained by others!

Issue - State: open - Opened by metazool 3 months ago - 5 comments

#46 - Workflow docs - addition of diagrams and one test fix

Pull Request - State: closed - Opened by metazool 3 months ago

#46 - Workflow docs - addition of diagrams and one test fix

Pull Request - State: closed - Opened by metazool 3 months ago

#45 - New plankton model available from Turing work

Issue - State: closed - Opened by metazool 3 months ago - 4 comments

#45 - New plankton model available from Turing work

Issue - State: closed - Opened by metazool 3 months ago - 4 comments

#44 - Alternative vector store to ChromaDB?

Issue - State: closed - Opened by metazool 3 months ago - 4 comments

#44 - Alternative vector store to ChromaDB?

Issue - State: closed - Opened by metazool 3 months ago - 4 comments

#43 - Pipeline issues (dependencies in tests, doc generation)

Issue - State: closed - Opened by metazool 3 months ago

#43 - Pipeline issues (dependencies in tests, doc generation)

Issue - State: closed - Opened by metazool 3 months ago

#42 - Documentation-only, focus on use of the object store

Pull Request - State: closed - Opened by metazool 4 months ago

#42 - Documentation-only, focus on use of the object store

Pull Request - State: closed - Opened by metazool 4 months ago

#41 - Special handling for flow cytometer images

Pull Request - State: closed - Opened by metazool 4 months ago

#41 - Special handling for flow cytometer images

Pull Request - State: closed - Opened by metazool 4 months ago

#40 - Add the Luigi pipeline for image decollaging

Pull Request - State: closed - Opened by metazool 4 months ago

#40 - Add the Luigi pipeline for image decollaging

Pull Request - State: closed - Opened by metazool 4 months ago

#39 - Handling for flow cytometer data format

Issue - State: closed - Opened by metazool 4 months ago

#39 - Handling for flow cytometer data format

Issue - State: closed - Opened by metazool 4 months ago

#38 - Luigi pipeline integration into this project

Issue - State: closed - Opened by metazool 4 months ago
Labels: demonstrate

#38 - Luigi pipeline integration into this project

Issue - State: closed - Opened by metazool 4 months ago
Labels: demonstrate

#37 - BioCLIP WIP notebook

Pull Request - State: closed - Opened by metazool 4 months ago - 1 comment

#36 - Options for setting up DVC for data / pipelines

Pull Request - State: closed - Opened by metazool 5 months ago

#36 - Options for setting up DVC for data / pipelines

Pull Request - State: closed - Opened by metazool 5 months ago

#35 - Add support for DVC, and switch out s3fs for boto3

Pull Request - State: closed - Opened by metazool 5 months ago

#35 - Add support for DVC, and switch out s3fs for boto3

Pull Request - State: closed - Opened by metazool 5 months ago

#34 - Shift from s3fs to boto3 for consistency

Issue - State: closed - Opened by metazool 5 months ago - 1 comment
Labels: improvement

#34 - Shift from s3fs to boto3 for consistency

Issue - State: closed - Opened by metazool 5 months ago - 1 comment
Labels: improvement

#33 - Deploy and improve the streamlit demo app

Issue - State: open - Opened by metazool 5 months ago - 2 comments
Labels: improvement, demonstrate

#32 - Packaged way adding a detritus classifier to image processing

Issue - State: open - Opened by metazool 5 months ago - 5 comments
Labels: demonstrate

#31 - Simple automation for the image decollage process

Issue - State: closed - Opened by metazool 5 months ago - 1 comment
Labels: demonstrate

#31 - Simple automation for the image decollage process

Issue - State: closed - Opened by metazool 5 months ago - 1 comment
Labels: demonstrate

#30 - Object store API for the plankton store in JASMIN

Issue - State: closed - Opened by metazool 5 months ago - 2 comments
Labels: improvement, demonstrate

#30 - Object store API for the plankton store in JASMIN

Issue - State: closed - Opened by metazool 5 months ago - 2 comments
Labels: improvement, demonstrate

#29 - Set things straight after the change to src layout

Pull Request - State: closed - Opened by metazool 5 months ago - 4 comments

#29 - Set things straight after the change to src layout

Pull Request - State: closed - Opened by metazool 5 months ago - 4 comments

#28 - Cleanup after the merge conflicts

Issue - State: closed - Opened by metazool 5 months ago - 2 comments
Labels: improvement

#28 - Cleanup after the merge conflicts

Issue - State: closed - Opened by metazool 5 months ago - 2 comments
Labels: improvement

#27 - Revert "Add the "decollage" process for raw microscope output to the package"

Pull Request - State: closed - Opened by jmarshrossney 6 months ago

#26 - Single-source pip and conda dependencies

Pull Request - State: closed - Opened by jmarshrossney 6 months ago - 5 comments

#25 - Confusion about the use of dask/xarray in this project

Issue - State: closed - Opened by jmarshrossney 6 months ago - 5 comments
Labels: question

#24 - Drop scivision

Pull Request - State: closed - Opened by jmarshrossney 6 months ago - 1 comment

#23 - Layout and minimal changes

Pull Request - State: closed - Opened by jmarshrossney 6 months ago - 2 comments

#22 - Add the "decollage" process for raw microscope output to the package

Pull Request - State: closed - Opened by metazool 6 months ago - 1 comment

#21 - Pipeline-runnable code to "decollage" the combined FlowCam images

Issue - State: closed - Opened by metazool 6 months ago - 3 comments

#21 - Pipeline-runnable code to "decollage" the combined FlowCam images

Issue - State: closed - Opened by metazool 6 months ago - 3 comments

#20 - Automating file transfer off the FlowCam

Issue - State: open - Opened by metazool 6 months ago - 4 comments
Labels: future

#19 - Clustering visualisation - notebook and basic streamlit demo

Pull Request - State: closed - Opened by metazool 6 months ago - 3 comments

#18 - Minimum change to reflect new bucket locations

Pull Request - State: closed - Opened by metazool 7 months ago - 4 comments

#18 - Minimum change to reflect new bucket locations

Pull Request - State: closed - Opened by metazool 7 months ago - 4 comments

#17 - FlowCam visit - documentation

Pull Request - State: closed - Opened by metazool 7 months ago - 1 comment

#17 - FlowCam visit - documentation

Pull Request - State: closed - Opened by metazool 7 months ago - 1 comment

#16 - Modest proposal for running a model on the FlowCam directly

Issue - State: open - Opened by metazool 7 months ago
Labels: future

#16 - Modest proposal for running a model on the FlowCam directly

Issue - State: open - Opened by metazool 7 months ago
Labels: future

#15 - Markdown representations of Jupyter notebooks

Pull Request - State: closed - Opened by jmarshrossney 7 months ago - 4 comments

#14 - Lockfiles

Issue - State: open - Opened by jmarshrossney 7 months ago - 8 comments
Labels: wontfix

#14 - Lockfiles

Issue - State: open - Opened by jmarshrossney 7 months ago - 8 comments
Labels: wontfix

#13 - Modify environment.yml

Pull Request - State: closed - Opened by jmarshrossney 7 months ago - 2 comments

#13 - Modify environment.yml

Pull Request - State: closed - Opened by jmarshrossney 7 months ago - 2 comments

#12 - Reflect layout changes to the object store

Issue - State: closed - Opened by metazool 7 months ago - 2 comments

#12 - Reflect layout changes to the object store

Issue - State: closed - Opened by metazool 7 months ago - 2 comments

#11 - Diagram view of first stage pipeline (from sampling instrument to shared storage)

Pull Request - State: closed - Opened by metazool 7 months ago - 1 comment

#11 - Diagram view of first stage pipeline (from sampling instrument to shared storage)

Pull Request - State: closed - Opened by metazool 7 months ago - 1 comment

#10 - Extract and store embeddings from BioCLIP

Issue - State: open - Opened by metazool 7 months ago - 3 comments
Labels: future, demonstrate

#9 - Higher-level system view walkthrough diagrams

Issue - State: open - Opened by metazool 7 months ago - 1 comment
Labels: documentation

#8 - Demo / lightning talk for plankton image data flow

Issue - State: closed - Opened by metazool 7 months ago - 4 comments
Labels: documentation

#7 - Quick attempt at model interpretation

Pull Request - State: closed - Opened by metazool 7 months ago - 5 comments

#6 - Apply model explainability tools to the images output by similarity search

Issue - State: closed - Opened by metazool 7 months ago - 3 comments
Labels: wontfix

#5 - Proof of concept of similarity search with the scivision model

Pull Request - State: closed - Opened by metazool 8 months ago - 6 comments

#4 - Minimal metadata for unlabelled images

Issue - State: open - Opened by metazool 8 months ago - 1 comment
Labels: documentation

#3 - Reading an image collection from s3 with intake

Issue - State: open - Opened by metazool 8 months ago - 1 comment
Labels: wontfix

#2 - Test lint and coverage workflows

Pull Request - State: closed - Opened by metazool 8 months ago - 2 comments

#1 - Test lint and coverage workflow Actions

Pull Request - State: closed - Opened by metazool 8 months ago - 1 comment

GitHub / nerc-ceh/plankton_ml issues and pull requests