From e90accaab528be56c4db61e9daec194bf69e14cf Mon Sep 17 00:00:00 2001 From: Conni Wetzker Date: Thu, 19 Mar 2026 13:49:07 +0100 Subject: [PATCH 1/2] Create index.md --- rfc/3/comments/3/index.md | 17 +++++++++++++++++ 1 file changed, 17 insertions(+) create mode 100644 rfc/3/comments/3/index.md diff --git a/rfc/3/comments/3/index.md b/rfc/3/comments/3/index.md new file mode 100644 index 00000000..ba6017f1 --- /dev/null +++ b/rfc/3/comments/3/index.md @@ -0,0 +1,17 @@ +# RFC-3: Comment 3 + +| **Role** | Name | GitHub Handle | Institution | +|----------|------|---------------|-------------| +| **Author** | [Cornelia Wetzker](https://orcid.org/0000-0002-8367-5163) | [cwetzker](https://github.com/cwetzker) | TU Dresden | + +I would like to contribute a further imaging modality to be considered in the current changes of the OME-Zarr format. Fluorescence lifetime imaging microscopy (FLIM) detects the fluorescence lifetime of fluorophores mostly in the pico- and nanosecond time range. This lifetime is assessed by detection of photon arrival times relative to the latest pulse of a pulsed laser. This date created so called decay histograms for each pixel/voxel of a dataset. This creates an additional dimension in the dataset. + +Since FLIM data is largely stored in proprietary file formats, the availability and access to analysis workflows is limited to date. + +Lifetime information could be included using the following metadata: + +```json +{ "name": "u", "type": "time", "unit": "nanoseconds" } +``` + +Lifetime is represented as time dimension which has to be carefully distinguished from the broadly used dimension of time, e.g. used for time-series. Datasets can have both time dimensions in case the lifetime is assessed in a time-series mode. From fc818036ef9fda39f1a5a2fe3c9e60cb012e8bbe Mon Sep 17 00:00:00 2001 From: Conni Wetzker Date: Thu, 19 Mar 2026 23:24:10 +0100 Subject: [PATCH 2/2] add a new comment to RFC-3 --- rfc/3/comments/3/index.md | 12 ++++++------ 1 file changed, 6 insertions(+), 6 deletions(-) diff --git a/rfc/3/comments/3/index.md b/rfc/3/comments/3/index.md index ba6017f1..289e8be4 100644 --- a/rfc/3/comments/3/index.md +++ b/rfc/3/comments/3/index.md @@ -4,14 +4,14 @@ |----------|------|---------------|-------------| | **Author** | [Cornelia Wetzker](https://orcid.org/0000-0002-8367-5163) | [cwetzker](https://github.com/cwetzker) | TU Dresden | -I would like to contribute a further imaging modality to be considered in the current changes of the OME-Zarr format. Fluorescence lifetime imaging microscopy (FLIM) detects the fluorescence lifetime of fluorophores mostly in the pico- and nanosecond time range. This lifetime is assessed by detection of photon arrival times relative to the latest pulse of a pulsed laser. This date created so called decay histograms for each pixel/voxel of a dataset. This creates an additional dimension in the dataset. +I would like to contribute a further imaging modality to be considered in the current and future changes of the OME-Zarr format. Fluorescence lifetime imaging microscopy (FLIM) is an imaging setup that detects the fluorescence lifetime of fluorophores as an additional axis of data using specialized laser, detector and electronics setups. This lifetime is assessed by detection of photon arrival times relative to the latest pulse of a pulsed laser. This creates so called decay histograms for each pixel/voxel of a dataset that can be considered an additional dimension or axis of the dataset and allows the calculation of the specific lifetime(s) of fluorescence. -Since FLIM data is largely stored in proprietary file formats, the availability and access to analysis workflows is limited to date. - -Lifetime information could be included using the following metadata: +The lifetime axis could be included using for example using the following axis metadata: ```json -{ "name": "u", "type": "time", "unit": "nanoseconds" } +{ "name": "u", "type": "time", "unit": "nanosecond" } ``` -Lifetime is represented as time dimension which has to be carefully distinguished from the broadly used dimension of time, e.g. used for time-series. Datasets can have both time dimensions in case the lifetime is assessed in a time-series mode. +The unit for the lifetime axis is typically nanoseconds, or milliseconds for more rarely performed phosphorescence lifetime imaging (PLIM). Consequently, this would require the option of a second axis of 'type:time'. There are technical setups that are capable to and use cases that may benefit from the generation of datasets that have both time axes, e.g. in case FLIM is performed in time-series mode. Consequently, there may be scenarios that create 6 dimensional datasets with xyzctu dimensions that exceed the current limitation of 5 axes for OME-Zarr arrays. + +Since FLIM data is partially stored in proprietary file formats, the availability and access to analysis workflows is limited to date. Thus, the possibility of storage of FLIM datasets in OME-Zarr format would increase the flexibility for data visualization and analysis options for imaging scientists and stimulate the development of analysis workflows that could be tailored to specific project needs if required.