Re: Trakem2- importing sequence as a grid

Posted by Saalfeld, Stephan on Nov 28, 2016; 3:37pm
URL: http://imagej.273.s1.nabble.com/Trakem2-importing-sequence-as-a-grid-tp5017596p5017643.html

Hi,

please find below a Python script that generates a zig-zag sequence
that can be imported as a text file

stepSizeY = 200
stepSizeZ = 1
nColumns = 10
nRows = 20
nSlices = 1000
fileformat = 'image_z%i_row%i_col%i.png'

for z in range(0, nSlices, stepSizeZ):
  for row in range(0, nRows, 2):
    # zig
    for col in range(0, nRows):
      print((fileformat + " %d %d %d") % (z, row, col, row * stepSizeY, col * stepSizeX, z))
    # zag
    for col in range(nRows - 1, -1, -1):
      print((fileformat + " %d %d %d") % (z, row + 1, col, row * stepSizeY + stepSizeY, col * stepSizeX, z))

Best,
Stephan


On Wed, 2016-11-23 at 21:29 +0200, Stoyan Pavlov wrote:

> I found a way around this:
> I feed the images to the MIST plugin (which is great but can't
> generate
> image greater than 2 GPx) and then I parse the global coordinates
> from the
> file generated by it to trakem2 (after editing to fit the trakem2
> conventions).
>
> Hopefully this will be solved soon however, because seems like a
> waste for
> processing time.
>
> Best wishes ,
>  Stoyan
>
> ---
> Dr. Stoyan P. Pavlov, MD, PhD
> Departament of Anatomy, Histology and Embryology
> Medical University "Prof. Dr. Paraskev Stoyanov", Varna
> Prof. Marin Drinov Str.55
> 9002 Varna
>  Bulgaria
> Tel: +359 (0) 52 - 677 - 052
> e-mail: [hidden email]
>            [hidden email]
>
> 2016-11-19 1:25 GMT+02:00 Stoyan Pavlov <[hidden email]>:
>
> >
> > Hi Stephan,
> > Thank you for your answer. I know about the text file import
> > feature.
> > The problem is that it is not that easy to generate the list: I am
> > talking
> > about more than 5000 images here.
> > The trakem2 manual btw was the first source I consulted.
> > Best regards
> > Stoyan
> >
> > ---
> > Dr. Stoyan P. Pavlov, MD, PhD
> > Departament of Anatomy, Histology and Embryology
> > Medical University "Prof. Dr. Paraskev Stoyanov", Varna
> > Prof. Marin Drinov Str.55
> > 9002 Varna
> >  Bulgaria
> > Tel: +359 (0) 52 - 677 - 052
> > e-mail: [hidden email]
> >            [hidden email]
> >
> > 2016-11-19 1:24 GMT+02:00 Stoyan Pavlov <[hidden email]>:
> >
> > >
> > > Hi Stephan,
> > > Thank you for your answer. I know about the text file import
> > > feature.
> > > The problem is that it is not that easy to generate the list: I
> > > am
> > > talking about more than 5000 images here.
> > > Best regards
> > > Stoyan
> > >
> > > ---
> > > Dr. Stoyan P. Pavlov, MD, PhD
> > > Departament of Anatomy, Histology and Embryology
> > > Medical University "Prof. Dr. Paraskev Stoyanov", Varna
> > > Prof. Marin Drinov Str.55
> > > 9002 Varna
> > >  Bulgaria
> > > Tel: +359 (0) 52 - 677 - 052
> > > e-mail: [hidden email]
> > >            [hidden email]
> > >
> > > 2016-11-18 18:07 GMT+02:00 Saalfeld, Stephan <[hidden email]
> > > hmi.org>
> > > :
> > >
> > > >
> > > > Hi,
> > > >
> > > > the easiest way to import custom acquisition patterns is to
> > > > generate an
> > > > import file and use "Import from text file".  It is very easy
> > > > to
> > > > generate such import file with e.g. Excel, OpenOffice Calc, or
> > > > the
> > > > scripting language of your choice if your pattern is moderately
> > > > regular.  If it's not, you have to do it anyways.  This
> > > > question has
> > > > been answered multiple times at various mailing lists but Web-
> > > > Search is
> > > > hard if you do not know the terms yet ;)
> > > >
> > > > Here they are: "import text file TrakEM2"
> > > >
> > > > Documentation is here
> > > >
> > > > https://www.ini.uzh.ch/~acardona/trakem2_manual.html#importing_
> > > > list
> > > >
> > > > Cheers,
> > > > Stephan
> > > >
> > > > On Fri, 2016-11-18 at 14:12 +0200, Stoyan Pavlov wrote:
> > > > >
> > > > > Dear friends,
> > > > > I recently started using TRAKEM2 for the stitching of
> > > > > microscopic
> > > > > mosaics.
> > > > > The thing I like the most is that it allows to export
> > > > > flattened
> > > > > (stitched
> > > > > and blended) image of any size. However I hit a bump and I
> > > > > hope
> > > > > someone can
> > > > > help:
> > > > > When I import sequence of images the tiles in every other row
> > > > > in the
> > > > > resulting grid are in reverse order. I guess the reason for
> > > > > this is
> > > > > that
> > > > > the plugin is importing the tiles in comb-like fashion. Is
> > > > > there a
> > > > > way to
> > > > > modify this behaviour in order to load the images in meander-
> > > > > like
> > > > > order,
> > > > > similarly to the sequential-continuous import in the MIST
> > > > > plugin (I
> > > > > like
> > > > > this plugin very much also, but unfortunately it doesn't
> > > > > allow the
> > > > > export
> > > > > of images >2 GPx).
> > > > > In other words TrakEM2 imports sequences now like this:
> > > > > 123
> > > > > 456
> > > > > 789
> > > > >
> > > > > Is there a way to force it to import them like this:
> > > > > 123
> > > > > 654
> > > > > 789
> > > > >
> > > > > Thank you in advance
> > > > >
> > > > > Stoyan
> > > > > ---
> > > > > Dr. Stoyan P. Pavlov, MD, PhD
> > > > > Departament of Anatomy, Histology and Embryology
> > > > > Medical University "Prof. Dr. Paraskev Stoyanov", Varna
> > > > > Prof. Marin Drinov Str.55
> > > > > 9002 Varna
> > > > >  Bulgaria
> > > > > Tel: +359 (0) 52 - 677 - 052
> > > > > e-mail: [hidden email]
> > > > >            [hidden email]
> > > > >
> > > > > --
> > > > > ImageJ mailing list: http://imagej.nih.gov/ij/list.html
> > > > --
> > > > ImageJ mailing list: http://imagej.nih.gov/ij/list.html
> > >
> > >
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html

--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html