From 95787ecf9438328069346b47d583ff038c1367c7 Mon Sep 17 00:00:00 2001 From: Marie-Helene Bourget Date: Thu, 16 Sep 2021 16:52:25 -0400 Subject: [PATCH 01/73] Initial commit adding Microscopy related files --- README.md | 1 + mkdocs.yml | 1 + src/02-common-principles.md | 1 + .../10-microscopy.md | 361 ++++++++++++++++++ .../images/microscopy_chunks.png | Bin 0 -> 136682 bytes .../images/microscopy_sem_overview.jpg | Bin 0 -> 169378 bytes src/99-appendices/04-entity-table.md | 4 + src/schema/datatypes/microscopy.yaml | 45 +++ src/schema/entities.yaml | 20 + 9 files changed, 433 insertions(+) create mode 100644 src/04-modality-specific-files/10-microscopy.md create mode 100644 src/04-modality-specific-files/images/microscopy_chunks.png create mode 100644 src/04-modality-specific-files/images/microscopy_sem_overview.jpg create mode 100644 src/schema/datatypes/microscopy.yaml diff --git a/README.md b/README.md index 41136e0fd3..69fe0beb5f 100644 --- a/README.md +++ b/README.md @@ -25,6 +25,7 @@ BIDS currently supports the following data modalities with more to come in the f - behavioral - physiological - PET +- Microscopy # Formatting your data with BIDS diff --git a/mkdocs.yml b/mkdocs.yml index 59c29c098a..7927fd923d 100644 --- a/mkdocs.yml +++ b/mkdocs.yml @@ -37,6 +37,7 @@ nav: - Behavioral experiments (with no neural recordings): 04-modality-specific-files/07-behavioral-experiments.md - Genetic Descriptor: 04-modality-specific-files/08-genetic-descriptor.md - Positron Emission Tomography: 04-modality-specific-files/09-positron-emission-tomography.md + - Microscopy: 04-modality-specific-files/10-microscopy.md - Derivatives: - BIDS Derivatives: 05-derivatives/01-introduction.md - Common data types and metadata: 05-derivatives/02-common-data-types.md diff --git a/src/02-common-principles.md b/src/02-common-principles.md index c8c5b306c6..4da3cad0b1 100644 --- a/src/02-common-principles.md +++ b/src/02-common-principles.md @@ -56,6 +56,7 @@ misunderstanding we clarify them here. 1. `ieeg` (intracranial electroencephalography) 1. `beh` (behavioral) 1. `pet` (positron emission tomography) + 1. `microscopy` Data files are contained in a directory named for the data type. In raw datasets, the data type directory is nested inside subject and diff --git a/src/04-modality-specific-files/10-microscopy.md b/src/04-modality-specific-files/10-microscopy.md new file mode 100644 index 0000000000..d2572cc6ec --- /dev/null +++ b/src/04-modality-specific-files/10-microscopy.md @@ -0,0 +1,361 @@ +# Microscopy + +Support for Microscopy was developed as a +[BIDS Extension Proposal](../07-extensions.md#bids-extension-proposals). + +Please see [Citing BIDS](../01-introduction.md#citing-bids) +on how to appropriately credit this extension when referring to it in the +context of the academic literature. + + +Microscopy datasets formatted using this specification are available on the +[BIDS examples repository](https://github.com/neuropoly/bids-examples/tree/bep031) +(`microscopy_SEM001` and `microscopy_SPIM001`) and can be used for practical +guidance when curating a new dataset. + +Further Microscopy datasets are available: + +- In PNG format: [`data_axondeepseg_sem`](https://doi.org/10.5281/zenodo.5498378) +- In OME-TIFF format: [link to the dataset - pending] + +## Microscopy recording data + +Template: +``` +sub-