#7 features for multipage tiff import

open
nobody
5
2014-08-20
2008-09-01
Dan White
No

here
http://idisk-srv1.mpi-cbg.de/~white/sample_data/LMFtest.zip

(let me jknow wha you got it, so i can take it down from there. )

is a common multipage Tiff formate we have here,
it is from Andor, which make fancy EM CCD sensitive cameras for spinning disk confocals and TIRF scopes.
There are very gooid camera, andf we have a very good relationship with them here.
(we get a new spinning disk from them this month, so we will have 2 of those plus the TIRF... lots of data)

The image data comes in a multipage TIFF file,
which can contain multiple colour channels,
z stacks, and usually time series.
16 bit Tiff, of which only 14 is actually used for image data (ir 2 more bits than 12 bit... watch out...)

In the file linked to above (from spinning disk confocal - 2 colour z stack time series)
the dimensioanlity order is

channel, z, time

so if you open the tiff in imageJ,
the first 2 slices are the fist z slices of the two colour channels.
then comes the next z slice for both channels, until all z slices are done, then this is repeated many times for each time point .
The .txt file contains as much meta info as the user should need to fill in the import dialog properly.

The tricky part here is the order of dimensionality,
and that there re 2 colour channels.

... so our import dialog would need some extra functionality to handle that.
It would be very handy to be able to specify the order of dimensionality in a multipage TIFF,
as it can vary as i describer above.

for instance sometimes in these files, for each z stack, the 2 colours are done one after the other/ consecutively,
so the dimensionality is
z, channel, time

and in TIRR the is only ever 1 z slice (its a 2D only method)
so the dimensionality is
colour , time

bio-formats reads this file correctly (i checked) and imaris also does.
... bio-fortmats open it in imageJ as
time, z, colour (as a separate stack if you like) ... which is a bit odd.... but there it is.

If we used bio-formats , i guess it would be easier to make it work properly......

but still, having a more versatile import function would be a nice feature.

cheers

Dan

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