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A tool to obtain relevant experimental parameters from a Prairie View (microscope acquisition program from Prairie Technologies)
formatted XML file contained with folders of Prairie View acquired TIFFs. Output is to stdout as well as a log file in the users python home directory.
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A python script to utilizing imagemagick and mencoder to convert subfolders of tiff sequences into avi movies. Requires that Imagemagick and mencoder are installed, and in the Windows system search path
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#a script to utilizing imagemagick and mencoder to convert subfolders of tiff sequences into avi movies. Requires that Imagemagick and mencoder are installed, and in the Windows system search path
#James Ackman March 3, 2010
importos, sys, glob, re, subprocess
#edit the following line for the location of the ImageMagick convert program. This is mainly for Windows where a identically named system tool for converting FAT32 to NTFS is located at c:\Windows\system32\convert.exe and can cause issues, even if ImageMagick directory is located first in your system path.
Convert a space delimited table on the system clipboard into markdown table, such as when copying tabular results from matlab or a spreadsheet or R command line. Written to use macos shell cmd pbpaste. But should be reworked to use xclip or similar as an option for linux. This script is most enjoyable when combined with a os wide shortcut, such …
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This applescript can be used to automatically draw on microscopic images in Adobe Photoshop as a new layer. This hasn't been tested in several years, but it depended on tiffutil to read the voxel-width from the tiff header in Leica confocal microscope files. TODO: Update and combine with the loci_tools.jar from OME project to make this more flex…
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--Select and open the image in the frontmost Finder window in Photoshop from which the Voxel-Width data can be obtained before proceeding performing the scale bar calculation. Must use Photoshop CS or Photoshop 7.0. Must change instances of "Photoshop CS" to "Photoshop 7.0" in this script and vice versa depending on which version you are using.
A simple applescript to fetch a bibliographic citation (using author, journal title, year) from pubmed.
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An ImageJ macro to make a dF/F movie from a calcium imaging recording.Works best if file extension is changed to '.ijm' and saved in your ImageJ folder at plugins/Macros/dFoverFmovie.ijm
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Brief command shell tutorial. Contains a few unix tips and tricks for working with and examining data files for science. A couple of the examples assume that the working environment is Mac OS X (e.g. pbcopy).
Instructions on converting a multimarkdown manuscript with mmd bibtex cite-keys and graphics into a Microsoft Word document with BibDesk cite-keys and graphics.
Convert multimarkdown manuscript to Microsoft Word document
Here are directions for converting a markdown/multimarkdown formatted text manuscript into a Microsoft Word document (unfortunately still a preferred format for submission to many journals). These directions will focus on turning bibtex citekeys (if you are using BibDesk or similar for references and bibliography management) from the [#citekey] format in multimarkdown to the \cite{citekey} format for use with BibDesk.app and BibDeskToWord.app to
This will use the Multimarkdown command line tool (mmd2odf) to create a flat open office document .fodt text file. Multimarkdown must be installed on your system. Alternatively pandoc can be used for this, but pandoc doesn't handle the nice multimarkdown table format as well and graphics can be messed up in resulting open office document .odt file.