General conversation regarding the processing of Light Microscopy inputs

[philipmac]

Need to evaluate a couple tools to do the conversion.

• Get all LM image file formats and evaluate the tools once on all of them instead of each time a new file format is requested.

• a front end for viewer the LM images which supports the false coloring.

Options include:

• Neuroglancer may be able to do it with some configurations.
• client side napari,
• fiji configured to use zarr.
• There may be components of OMERO which would be useful to us.
• https://github.com/imagej/pyimagej

[philipmac]

One type of image file will derive from Nanostring. (This will be priority for LM for now.) Need an example of this.

[blowekamp]

The long standing tool for reading LM image files is OME bioformats which primarily outputs OME-TIFF files. Current work from OME is on OME-NGFF ( based on zarr).

There is also SCIFIO from the imagej community: https://scif.io

[philipmac]

Additionally there will be a 2D CZI output deriving from Nanostring machines. Can czi file be displayed natively within FIJI? or do we always want to convert them to some intermed format.

(Note - imageJ is the existing tool they are familiar with using.)

[blowekamp]

Will the Hedwig users be exposed to file format? Does it matter to them?

[philipmac]

closing - current decision is to use Neuroglancer & OME-Zarr (created using bioformats2raw).

Will create new discussion consolidating czi input processing and specifications.