Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Optophysiology project and goals #108

Open
wants to merge 5 commits into
base: main
Choose a base branch
from
Open

Optophysiology project and goals #108

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
5 commits
Select commit Hold shift + click to select a range
c06974e
Add draft description
lauraporta Nov 28, 2024
613c1fc
Add derotation (should we?) | sphinx-build breaks 🐛
lauraporta Nov 28, 2024
208e07d
Change name
lauraporta Dec 9, 2024
005c156
Fix icon name
lauraporta Dec 9, 2024
04d320d
Fix broken links
lauraporta Dec 9, 2024
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
4 changes: 2 additions & 2 deletions docs/source/blog/neuroblueprint.md
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -153,7 +153,7 @@ levels. The naming of these folders should adhere to a certain style, as exempli
<br>

While the full specification is available to read
[here](https://neuroblueprint.neuroinformatics.dev/specification.html),
[here](https://neuroblueprint.neuroinformatics.dev/latest/specification.html),
we provide a brief summary of its main features:

- A top-level distinction splitting raw data ("rawdata") and data derived from processing the raw data ("derivatives")
Expand All @@ -173,7 +173,7 @@ but recommendations for these are in development.
### Getting Started

Getting started with **NeuroBlueprint** is as easy as reading the
[specification](https://neuroblueprint.neuroinformatics.dev/specification.html), and organising your experimental
[specification](https://neuroblueprint.neuroinformatics.dev/latest/specification.html), and organising your experimental
folders according to the standard. It's recommended to get started by using **NeuroBlueprint** with your
next experiment, rather than trying to re-organise existing folders and analysis code, which is always tricky.

Expand Down
21 changes: 21 additions & 0 deletions docs/source/projects.md
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -51,6 +51,27 @@ test different pipeline configurations.
:::
::::


(projects-optophysiology)=
## Optophysiology
::::{grid} 1 1 1 1
:::{grid-item-card} {fas}`sun;sd-text-primary` PhotonMosaic
Copy link
Member

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

To match the repo

Suggested change
:::{grid-item-card} {fas}`sun;sd-text-primary` PhotonMosaic
:::{grid-item-card} {fas}`sun;sd-text-primary` photon-mosaic

:link: https://github.com/neuroinformatics-unit/photon-mosaic
PhotonMosaic simplifies the analysis of multi-photon calcium imaging data by integrating algorithms from tools like Suite2p and Caiman into a modular pipeline. Researchers can evaluate, compare, and combine methods for each processing step, such as registration or source extraction, and explore metrics to identify the best fit for their datasets.
Copy link
Member

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

Suggested change
PhotonMosaic simplifies the analysis of multi-photon calcium imaging data by integrating algorithms from tools like Suite2p and Caiman into a modular pipeline. Researchers can evaluate, compare, and combine methods for each processing step, such as registration or source extraction, and explore metrics to identify the best fit for their datasets.
PhotonMosaic simplifies the analysis of multi-photon calcium imaging data by integrating algorithms from tools like Suite2p and CaImAn into a modular pipeline. Researchers can evaluate, compare, and combine methods for each processing step, such as registration or source extraction, and explore metrics to identify the best fit for their datasets.

Copy link
Member

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

Suggested change
PhotonMosaic simplifies the analysis of multi-photon calcium imaging data by integrating algorithms from tools like Suite2p and Caiman into a modular pipeline. Researchers can evaluate, compare, and combine methods for each processing step, such as registration or source extraction, and explore metrics to identify the best fit for their datasets.
photon-mosaic simplifies the analysis of multi-photon calcium imaging data by integrating algorithms from tools like Suite2p and Caiman into a modular pipeline. Researchers can evaluate, compare, and combine methods for each processing step, such as registration or source extraction, and explore metrics to identify the best fit for their datasets.


With support for local or cluster-based parallelization, PhotonMosaic provides visualization tools, reports, and guides to streamline decision-making and enhance reproducibility.
Copy link
Member

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

Suggested change
With support for local or cluster-based parallelization, PhotonMosaic provides visualization tools, reports, and guides to streamline decision-making and enhance reproducibility.
With support for local or cluster-based parallelization, photon-mosaic provides visualization tools, reports, and guides to streamline decision-making and enhance reproducibility.

:::
::::

::::{grid} 1 1 1 1
:::{grid-item-card} {fas}`stroopwafel;sd-text-primary` derotation
:link: https://github.com/neuroinformatics-unit/derotation
A python library to solve sample-rotation artifacts on movies acquired with a line scanning microscope.
Copy link
Member

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

Suggested change
A python library to solve sample-rotation artifacts on movies acquired with a line scanning microscope.
A python library to solve sample-rotation artifacts in multiphoton imaging data acquired with a line scanning microscope.

:::
::::



(projects-data-management)=
## Data Management
::::{grid} 1 1 1 1
Expand Down
2 changes: 1 addition & 1 deletion docs/source/roadmaps/june-2024.md
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -19,7 +19,7 @@ longer-term goal of multimodal integration. The detailed roadmap is split into t
We have developed [NeuroBlueprint](https://neuroblueprint.neuroinformatics.dev/), a simple, standard data folder
specification for (systems) neuroscience and [datashuttle](https://datashuttle.neuroinformatics.dev/), to automate the
creation, validation and transfer of NeuroBlueprint projects. For more details on these specific projects, see the
[NeuroBlueprint](https://neuroblueprint.neuroinformatics.dev/roadmap.html) and
[NeuroBlueprint](https://neuroblueprint.neuroinformatics.dev/latest/roadmap.html) and
[datashuttle](https://datashuttle.neuroinformatics.dev/pages/community/roadmap.html) roadmaps.

**Q4 2024**
Expand Down
Loading