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IJ2-python-lib

2,770 bytes removed, 13:31, 13 December 2016
Replaced content with "Now integrated to https://github.com/hadim/fiji_scripts"
{{Infobox| name = ij2-python-lib| logo = | software = Fiji| author = {{Person|Hadim}}| maintainer = {{Person|Hadim}}| source = {{GitHub|org=hadim|repo=ij2-python-lib}}| released = 15/11/2016| status = v0.1.0, development| category = }}__TOC__ == Presentation == ''ij2-python-lib'' is a set of IJ2 Python Libraries. Note that this library has been designed to regroup useful functions the author use often. And so many functions are very specific to the use-case of the author. == Install == Add the ''Hadim'' update site in ''Help ▶ Update…'' (see http://imagej.net/Following_an_update_site for details on how Now integrated to proceed). == Documentation == The best documentation is [https://github.com/hadim/ij2-python-lib/tree/master/src/main/resources/ij2_tools the source code]. Some functions have <code>ij</code> has a first argument, it excepts to receive an <code>ImageJ</code> object.  <source lang="python"># Do a maximum Z projectionfrom ij2_tools.z_projection import do_z_projectiondo_z_projection(ij, data, save=False, output_dir="") # Apply a DOG filterfrom ij2_tools.dog_filtering import apply_dog_filterapply_dog_filter(ij, data, sigma1, sigma2, save=False, output_dir="") # Apply automatic threshold on an image# Method is string representing available algorithm in `ops.threshold`from ij2_tools.threshold import do_thresholddo_threshold(ij, data, method, k1=1, save=False, output_dir="") # Subtract the first image of a stack to the entire stackfrom ij2_tools.subtract import subtract_first_imagesubtract_first_image(ij, data, save=False, output_dir=""): # Print dataset dimensions for X, Y, Z, TIME and CHANNELfrom ij2_tools.ij_utils import print_info # Check if a point is inside a circlefrom ij2_tools.geometry import in_circlein_circle(point, center, radius) # Return the points defining a circlefrom ij2_tools.geometry import get_circle_pointsget_circle_points(x_center, y_center, radius, n=20) # Return the points defining the association of two circlesfrom ij2_tools.geometry import get_two_circles_pointsget_two_circles_points(x1, y1, x2, y2, radius, n=20) # Detect spots using the TrackMate DOG Detectorfrom ij2_tools.spot_detector import dog_detectordog_detector(ij, data, radius, relative_threshold=1, doSubpixel=True, doMedian=False, calibration=None) # Return the IJ1 ROI Managerfrom ij2_tools.ij1 import get_roi_managerget_roi_manager(new=False)</source> == Related links ==* Source code on GitHub : https://github.com/hadim/ij2-python-lib == Authors == ''ij2-python-lib'' has been created by Hadrien Mary. This work started in 2016 at the Gary Brouhard laboratory (http://brouhardlab.mcgill.ca) at McGill University.fiji_scripts
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