Trakem2- importing sequence as a grid
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Trakem2- importing sequence as a grid
 
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Re: Trakem2- importing sequence as a grid
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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 |
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Re: Trakem2- importing sequence as a grid
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Re: Trakem2- importing sequence as a grid
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Re: Trakem2- importing sequence as a grid
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Re: Trakem2- importing sequence as a grid
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In reply to this post by Stoyan Pavlov
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 |
Re: Trakem2- importing sequence as a grid
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