From 8dd97da30e42173aa4245a779d433876f121003e Mon Sep 17 00:00:00 2001 From: GaelleChapuis Date: Mon, 20 May 2024 20:23:55 +0000 Subject: [PATCH] adding new project --- .../README.md | 50 +++++++++++++++++++ .../src/README.md | 1 + 2 files changed, 51 insertions(+) create mode 100644 projects/spike_net:_create_benchmark_datasets_by_manually_picking_visible_spikes/README.md create mode 100644 projects/spike_net:_create_benchmark_datasets_by_manually_picking_visible_spikes/src/README.md diff --git a/projects/spike_net:_create_benchmark_datasets_by_manually_picking_visible_spikes/README.md b/projects/spike_net:_create_benchmark_datasets_by_manually_picking_visible_spikes/README.md new file mode 100644 index 0000000..c35207c --- /dev/null +++ b/projects/spike_net:_create_benchmark_datasets_by_manually_picking_visible_spikes/README.md @@ -0,0 +1,50 @@ +# Project title: +Spike Net: Create benchmark datasets by manually picking visible spikes +### Key Investigators + +* Gaelle Chapuis, Olivier Winter, Alessio Buccino +* (all the code comes from Olivier Winter !) + +## Project Description +To assess the precision and recall of a spike sorter spike detection, there are a few approaches - hybrid datasets, ground truth datasets with intracellular recordings performed juxtacellularly ; but these datasets are either missing some natural components, or are rare. +Here we propose to enhance our pool of dataset by having humans labelling visible spikes on raw data, recorded in several brain regions. + +### Background + +viewephys is a viewer of raw ephys data developed by Olivier Winter at the International Brain Laboratory: +https://github.com/int-brain-lab/viewephys + +We propose to develop the benchmarks using the IBL datasets publicly available: +http://reveal.internationalbrainlab.org.s3-website-us-east-1.amazonaws.com/benchmarks.html#/0/2 +Loading code: https://int-brain-lab.github.io/iblenv/notebooks_external/loading_raw_ephys_data.html + +### Objectives +The main work at this hackathon will focus on documenting and amending the viewephys desktop app to perform manual spike picking -- from there, it can be later input into a web platform (but this will not be done at this Hackathon). + +### Approach and Plan + +Fill in with approach and project plan + + * [ ] Task 1: download data for one IBL raw data snippet, launch the view into the GUI + * [ ] Task 2: pick a few spikes, save and reload --> write all the code and documentation for this, so someone else can redo it [some functions may require changes, especially if we want to label visible clusters] + * [ ] Task 3: finish the picking for one insertion (if not more) + * [ ] Task 4: (if time allows): mesure precision and recall from spike sorting on this particular snippet of data + +### Progress + +Fill in with tentative milestones (or leave blank for later): + + * [ ] Milestone 1 : documentation of picking for others to do as well (ideally someone else would have tried doing it to validate this milestone) + * [ ] Milestone 2 : 1 snippet finished + * [ ] Milestone 3 : mesure quality of a spike sorter detection on this snippet + +### Next Steps (optional) + +- Liase with others in the community to do the spike picking +- See if someone would be interested to port this into a web application +- Discuss where the spike picking datasets should be saved ? + +## References + +Spike net: https://docs.google.com/document/d/1OA69Ptg58AQnGdmGi6UvZFrngwZDMixil1V7hJX6bNI/edit + diff --git a/projects/spike_net:_create_benchmark_datasets_by_manually_picking_visible_spikes/src/README.md b/projects/spike_net:_create_benchmark_datasets_by_manually_picking_visible_spikes/src/README.md new file mode 100644 index 0000000..80ea5e8 --- /dev/null +++ b/projects/spike_net:_create_benchmark_datasets_by_manually_picking_visible_spikes/src/README.md @@ -0,0 +1 @@ +Add your code here