Skip to content

Commit

Permalink
Update latest to 0.2
Browse files Browse the repository at this point in the history
  • Loading branch information
@constantinpape
constantinpape committed Apr 26, 2021
1 parent 4fff9da commit bba6940
Showing 1 changed file with 63 additions and 21 deletions.
84 changes: 63 additions & 21 deletions latest/index.bs
View file
Original file line number Diff line number Diff line change
Expand Up @@ -2,10 +2,9 @@
Title: Next-generation file formats (NGFF)
Shortname: ome-ngff
Level: 1
Status: LS-COMMIT
Status: w3c/ED
Status: w3c/CG-FINAL
Group: ome
URL: https://ngff.openmicroscopy.org/latest/
URL: https://ngff.openmicroscopy.org/0.2/
Repository: https://github.com/ome/ngff
Issue Tracking: Forums https://forum.image.sc/tag/ome-ngff
Logo: http://www.openmicroscopy.org/img/logos/ome-logomark.svg
Expand All @@ -18,12 +17,12 @@ Editor: Sébastien Besson, Open Microscopy Environment (OME) https://www.openmic
Abstract: This document contains next-generation file format (NGFF)
Abstract: specifications for storing bioimaging data in the cloud.
Abstract: All specifications are submitted to the https://image.sc community for review.
Status Text: The current released version of this specification is
Status Text: <a href="../0.1/index.html">0.1</a>. Migration scripts
Status Text: will be provided between numbered versions. Data written with these latest changes
Status Text: This is the 0.2 release of this specification. Migration scripts
Status Text: will be provided between numbered versions. Data written with the latest version
Status Text: (an "editor's draft") will not necessarily be supported.
</pre>


Introduction {#intro}
=====================

Expand Down Expand Up @@ -127,10 +126,11 @@ multiple levels of resolutions and optionally associated labels.
│ ├── .zarray # All image arrays are 5-dimensional
│ │ # with dimension order (t, c, z, y, x).
│ │
│ ├── 0.0.0.0.0 # Chunks are stored with the flat directory layout.
│ │ ... # Each dotted component of the chunk file represents
│ └── t.c.z.y.x # a "chunk coordinate", where the maximum coordinate
│ # will be `dimension_size / chunk_size`.
│ └─ t # Chunks are stored with the nested directory layout.
│ └─ c # All but the last chunk element are stored as directories.
│ └─ z # The terminal chunk is a file. Together the directory and file names
│ └─ y # provide the "chunk coordinate" (t, c, z, y, x), where the maximum coordinate
│ └─ x # will be `dimension_size / chunk_size`.
│
└── labels
│
Expand Down Expand Up @@ -207,8 +207,48 @@ keys as specified below for discovering certain types of data, especially images

Metadata about the multiple resolution representations of the image can be
found under the "multiscales" key in the group-level metadata.
The specification for the multiscale (i.e. "resolution") metadata is provided
in [zarr-specs#50](https://github.com/zarr-developers/zarr-specs/issues/50).

"multiscales" contains a list of dictionaries where each entry describes a multiscale image.

Each "multiscales" dictionary MUST contain the field "datasets", which is a list of dictionaries describing
the arrays storing the individual resolution levels.
Each dictionary in "datasets" MUST contain the field "path", whose value contains the path to the array for this resolution relative
to the current zarr group. The "path"s MUST be ordered from largest (i.e. highest resolution) to smallest.

It SHOULD contain the field "name".

It SHOULD contain the field "version", which indicates the version of the
multiscale metadata of this image (current version is 0.2).

It SHOULD contain the field "type", which gives the type of downscaling method used to generate the multiscale image pyramid.
It SHOULD contain the field "metadata", which contains a dictionary with additional information about the downscaling method.

```json
{
"multiscales": [
{
"version": "0.2",
"name": "example",
"datasets": [
{"path": "0"},
{"path": "1"},
{"path": "2"}
],
"axes": [
"t", "c", "z", "y", "x"
],
"type": "gaussian",
"metadata": { # the fields in metadata depend on the downscaling implementation
"method": "skimage.transform.pyramid_gaussian", # here, the paramters passed to the skimage function are given
"version": "0.16.1",
"args": "[true]",
"kwargs": {"multichannel": true}
}
}
]
}
```

If only one multiscale is provided, use it. Otherwise, the user can choose by
name, using the first multiscale as a fallback:

Expand All @@ -223,9 +263,6 @@ if not datasets:
datasets = [x["path"] for x in multiscales[0]["datasets"]]
```

The subresolutions in each multiscale are ordered from highest-resolution
to lowest.

"omero" metadata {#omero-md}
----------------------------

Expand All @@ -235,7 +272,7 @@ can be found under the "omero" key in the group-level metadata:
```json
"id": 1, # ID in OMERO
"name": "example.tif", # Name as shown in the UI
"version": "0.1", # Current version
"version": "0.2", # Current version
"channels": [ # Array matching the c dimension size
{
"active": true,
Expand Down Expand Up @@ -312,7 +349,7 @@ above).
```json
"image-label":
{
"version": "0.1",
"version": "0.2",
"colors": [
{
"label-value": 1,
Expand Down Expand Up @@ -424,7 +461,7 @@ For example the following JSON object defines a plate with two acquisition and
"name": "B"
}
],
"version": "0.1",
"version": "0.2",
"wells": [
{
"path": "2020-10-10/A/1"
Expand Down Expand Up @@ -491,7 +528,7 @@ the last two fields of view were part of the second acquisition.
"path": "3"
}
],
"version": "0.1"
"version": "0.2"
}
```

Expand Down Expand Up @@ -534,9 +571,9 @@ Note: If you would like to see your project listed, please open an issue or PR o
Citing {#citing}
================

[Next-generation file format (NGFF) specifications for storing bioimaging data in the cloud.](https://ngff.openmicroscopy.org/0.1)
[Next-generation file format (NGFF) specifications for storing bioimaging data in the cloud.](https://ngff.openmicroscopy.org/0.2)
J. Moore, *et al*. Editors. Open Microscopy Environment Consortium, 20 November 2020.
This edition of the specification is [https://ngff.openmicroscopy.org/0.1/](https://ngff.openmicroscopy.org/0.1/]).
This edition of the specification is [https://ngff.openmicroscopy.org/0.2/](https://ngff.openmicroscopy.org/0.2/]).
The latest edition is available at [https://ngff.openmicroscopy.org/latest/](https://ngff.openmicroscopy.org/latest/).
[(doi:10.5281/zenodo.4282107)](https://doi.org/10.5281/zenodo.4282107)

Expand All @@ -551,6 +588,11 @@ Version History {#history}
<td>Description</td>
</tr>
</thead>
<tr>
<td>0.2.0</td>
<td>2021-03-29</td>
<td>Change chunk dimension separator to "/" </td>
</tr>
<tr>
<td>0.1.4</td>
<td>2020-11-26</td>
Expand Down

0 comments on commit bba6940

Please sign in to comment.