[chimerax-users] Bio-Formats with ChimeraX?

[Matthew Akamatsu]

Hi Tom,

Thanks very much for your reply. I am interested in helping out however I
can (probably with test use cases) as ChimeraX seems like the best hope to
handle and render large 4D-5D optical microscopy data (e.g. the flood of
data coming from lattice light sheet microscopes). So far I have noticed
that if I try to open a TIFF hyperstack larger than ~3GB it opens as a
single plane instead, even if I increase the dataCacheSize to 15000-25000
MB on my 32GB RAM machine with a fast SSD drive (reads at 2.5 GB/s). I
tried saving the file in other TIF based formats like ome TIFF and have not
had any luck.  I am happy to try to share an example file, or take any
other suggestions you have for other formats I should try to save the
movies as before loading them into ChimeraX.


Matt




On Thu, Feb 7, 2019 at 12:06 PM Tom Goddard <goddard at sonic.net> wrote:

> Hi Matt,
>
>   ChimeraX tries to handle multi-channel, multi-time TIFFs such as OME
> TIFF and ImageJ TIFF.  I am interested in seeing examples where that is not
> working as I’d definitely like to improve ChimeraX for 3D optical
> microscopy.  Handling the many optical microscopy formats is a big problem,
> I think bioformats reads over 100 formats many of them proprietary from
> microscope vendors.  The trouble is bioformats is written in Java and
> ChimeraX is Python and C++.  It is hard to integrate Java with Python.  I
> looked at solutions for this specifically to make use of bioformats but a
> year ago it looked like this would both require shipping some poorly
> supported Java/Python interoperability with ChimeraX, either requiring
> users to install Java (which will greatly limit the number people who will
> ever use it) or including a Java which would make ChimeraX downloads even
> more enormous, and even accepting all that the speed reading the very large
> optical microscopy data would like be glacial.  So it didn’t look feasible
> with the limited resources we have to develop ChimeraX.  If you think there
> is a way I missed, tell me.
>
>   So my strategy is to go with the lowest common denominator in optical
> microscopy which is TIFF.  TIFF is a horrible format for performance with
> 3D-5D data — it is designed for sets of 2D images and those are in a linked
> list in the file where you cannot simply jump to the 1000th 2D image
> without reading the first 999 images.  That isn’t always true, some formats
> (e.g. MicroManager tiff) create an index in the TIFF header so they can
> find the 2d images efficiently.  At any rate, TIFF is the common exchange
> format.  For higher performance my effort has been to use HDF5 which is
> specifically intended for high performance with large multidimensional
> arrays.  There are many formats based on HDF5 like Imaris *.ims files or
> .minc files used in optical microscopy.  But there is no standard HDF5
> format — it is basically just a directory structure for numeric arrays in a
> single file and to define an HDF5 format you need to know what that
> directory structure in the file looks like.  About 10 years ago I used HDF5
> to make a format called Chimera map format (suffix *.cmap) for electron
> microscopy.  ChimeraX reads and writes that (and also will read IMS format
> and EMAN HDF5).  Chimera map format is what I use when I want to process 3d
> multichannel optical microscopy time series.  But it turns out HDF5 often
> has very poor speed, 5x or more times slower than expected.  HDF5 is pretty
> complex, it tiles the data, can compress individual tiles, it has caches to
> keep recently used tiles in memory.  Your code can control all the
> parameters (like tile size, cache sizes) and ChimeraX sometimes sets those,
> or HDF5 will use defaults.  Either way it is very common to get very poor
> performance due to reading tiles from all over the disk (fragmentation of
> 3d arrays), or HDF5 running out of cache and reading tiles over and over
> and over, or you try to get one slice and reads 50x times more data because
> the tiles to cover that slice are 50 slices thick.  Sadly, the main way to
> compensate for this is to use a fast SSD drive, current ones can read at 3
> Gbytes/second instead of spinning drives at 0.1 Gbytes/second.
>
>   I’m interested in improving ChimeraX for optical microscopy but we have
> little time and little (really no) funding for that so if you have
> suggestions they need to confer maximum benefit for minimum effort to have
> a chance of getting implemented.
>
>         Tom
>
>
> > On Feb 6, 2019, at 9:02 PM, Matthew Akamatsu wrote:
> >
> > Hi,
> >
> > I just started using ChimeraX to render and save 3D time lapse
> microscopy data as a high-performance replacement of Fiji. I am wondering
> how flexible ChimeraX can be in opening different TIF-derived file formats
> - particularly hyperstacks (multi color, multi Z, multi time). Other
> desired formats would be proprietary formats like .nd2 and .sld .
> Bio-Formats does all of this in an open-source manner - how feasible would
> it be to have bio-formats type functionality in ChimeraX?
> >
> > Thanks,
> > Matt
> >
> >
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>

-- 
Matthew Akamatsu, PhD
Arnold O. Beckman Postdoctoral research fellow, Drubin lab
University of California at Berkeley
Department of Molecular and Cellular Biology
510-642-0940
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