[MINC-users] TIFF to MINC?

[Andrew Janke]

Hi Gabriel,

If these are relatively simple tiff files, have a look at img2mnc.

   https://github.com/BIC-MNI/minc-widgets/blob/master/img2mnc/img2mnc

it's essentially mincpik turned upside down.

However in the microscopy world tiff can take a number of meanings,
OME TIFF is probably the most common in which a large amount of extra
metadata is included. These are generated by the bioformats library
(Omero), it's java based so you need to get familiar with it, the tool
you want is bfconvert. Think of it as imagemagick for microscopy.

OME Tiff files and other TIFF files in microscopy are often also tiled
or what is called a bigtiff, these won't be read by traditional tools
that read tiff files or perhaps they will but you'll only get the
first frame/layer/chanel, for these you can either use bfconvert to
get them to PNG or there is a small C tool that Claude wrote for
bigtiff to minc. I have the code for this but haven't put it on github
yet. let me know if you need it.

On this note bioformats does have rudimentary read support for MINC, I
currently have a project underway with the Omero group to incorporate
better HDF5/MINC support within bioformats/omero. 3D data support is
not done well in OMERO so I'm working with them to make MINC/HDF5 the
answer to this.

ta

a



On 6 December 2016 at 04:09, Gabriel A. Devenyi
<gabriel.devenyi at mcgill.ca> wrote:
> I've got my hands on some autofluorescence data from a two-photon
> microscope that I'd like to convert into a MINC volume. Right now I have a
> stack aligned TIFF files.
>
> Has anyone tried something like this before and can share their process,
> otherwise, I'll try and document the final conversion process I figure out.
>
> Thanks.
>
> --
> Gabriel A. Devenyi B.Eng. Ph.D.
> Research Computing Associate
> Computational Brain Anatomy Laboratory
> Cerebral Imaging Center
> Douglas Mental Health University Institute
> McGill University
> t: 514.761.6131x4781
> e: gabriel.devenyi at mcgill.ca
> _______________________________________________
> MINC-users at bic.mni.mcgill.ca
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