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Task #13136 (new)

Opened 4 years ago

Last modified 4 years ago

Add support for Berthold Nightshade data

Reported by: mlinkert Owned by:
Priority: major Milestone: Unscheduled
Component: Bio-Formats Version: n.a.
Keywords: new-format, external Cc: rmunoz@…
Resources: n.a. Referenced By: n.a.
References: n.a. Remaining Time: n.a.
Sprint: n.a.

Description

See QA 16964 and https://www.berthold.com/en/bio/in_vivo_plant_imager_NightSHADE_LB985.

From Rubén Muñoz:


The reason why I write you is that we purchased a relatively new system from
Berthold technologies, which is called NightShade?. Unfortunately this
system stores images in a database format which only permits jpg export of
the previsualization data. Raw data and metadata storage formats is unknown
to us.


We'll likely need screenshots/exports before we can start work on this, since we don't have a lot of support for in-vivo imagers and the format doesn't appear to be based on something we already support.

Change History (4)

comment:1 Changed 4 years ago by mlinkert

See also QA 16967.

comment:2 Changed 4 years ago by mlinkert

See also QA 16975.

comment:3 Changed 4 years ago by jamoore

  • Milestone changed from 5.x to Unscheduled

comment:4 Changed 4 years ago by mlinkert

  • Owner mlinkert deleted

Each of the above QAs is a pair of zips - one with the real NightShade? dataset and one with the same dataset exported to TIFF (for QA 16975, this is a partial export of the 005 directory only).

As far as I can tell, each plane ("sequence"?) in the original dataset is split into its own folder (e.g. 005/1/); each folder appears to contain 2 channels (fluor or lumin and photo). Each channel should be represented by 3 files - .dat, .lut, and .owl - which look like XML (corresponding to the exported .xml file), lookup table data, and raw data respectively. The .owl file also seems to have an XML footer after the raw (double-precision?) data; the image dimensions can be taken from the .dat file. All of the other files in the plane folder should go on the used file list, but can likely be ignored otherwise.

This will be a slightly more complex format to support, so I'd suggest against doing this until you've written at least one other reader. Do be prepared to spend some quality time with a hex editor, but as the pixel data appears to be uncompressed and each plane is in it's own file (i.e. finding offsets should be straightforward) this is also far from the worst thing we've seen.

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