Converter page - Githubissues

UQ-RCC / ipp

The IPP is a Web portal for biologists to interact with High Performance Compute (HPC) systems. Designed and funded by the IMB Microscopy Facility & the Research Computing Centre (RCC)

https://rcc.uq.edu.au/

MIT License

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Converter page #29

Open IMBMicroscopy opened 2 years ago

IMBMicroscopy commented 2 years ago

dropdown with a list of converters to use

.ims to tif .sld to tif ...

DrSpringy commented 2 years ago

User can select one file or multiple files  to convert in a single job

Use metadata scrapers/Bioformats to Auto-detect file format and use appropriate converter automatically 

if a scraper isnt available for that format currently fall back to Bio-Formats?

User selects what output format,shape etc they want using checkboxes 

Output format
- .tif
- ome-tif
- ome-zarr
- .ims
- arivis
- etc
Single File OR
Split scenes/series
Split timepoints 
Split channels 
Split Z-stacks

Options

Use Channel Names
Append Additional Metadata to output file
Generate separate .xml metadata file
Sub-folder per Split
compress output
- .tar
- .zip
Send Copy To
- Napari (DASK array)
- FIJI

DrSpringy commented 2 years ago

https://napari.org/tutorials/applications/dask.html

DrSpringy commented 5 months ago

It's currently not obvious what the converter page is for, or what it does, we need to atleast clarify that if nothing else

NickCondon commented 4 months ago

https://github.com/sebi06/czitools

could be useful to implement a czi > ome zarr converter

DrSpringy commented 4 months ago

👍 Please excuse my brevity as I'm on my phone.

On 13 Feb 2024, at 10:51 am, Nicholas Condon @.***> wrote:

https://github.com/sebi06/czitools

could be useful to implement a czi > ome zarr converter

— Reply to this email directly, view it on GitHubhttps://github.com/UQ-RCC/ipp/issues/29#issuecomment-1939939013, or unsubscribehttps://github.com/notifications/unsubscribe-auth/AVRN76FPWZ37YBMEM3GM2CDYTK2HDAVCNFSM5DFWYOIKU5DIOJSWCZC7NNSXTN2JONZXKZKDN5WW2ZLOOQ5TCOJTHE4TGOJQGEZQ. You are receiving this because you commented.Message ID: @.***>

markendr commented 3 months ago

JS, NC, DG, ND, ME zoom call on 27-Mar-2024:

Drop-down list to select and run configured converter tools JS attached list of tools attached to another issue, find and xref here ImageJ and other software have example pages with standard form to run similar tools ME to check with Oliver on slidebook tool