Revision as of 17:57, 15 November 2016 by Hadim (talk | contribs)
Revision as of 17:57, 15 November 2016 by Hadim (talk | contribs)
ij2-python-lib (Fiji)
Author Hadrien Mary
Maintainer Hadrien Mary
Source on GitHub
Initial release 15/11/2016
Development status v0.1.0, development



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.


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The best documentation is the source code.

Some functions have ij has a first argument, it excepts to receive an ImageJ object.

# Do a maximum Z projection
from ij2_tools.z_projection import do_z_projection
do_z_projection(ij, data, save=False, output_dir="")

# Apply a DOG filter
from ij2_tools.dog_filtering import apply_dog_filter
apply_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_threshold
do_threshold(ij, data, method, k1=1, save=False, output_dir="")

# Subtract the first image of a stack to the entire stack
from ij2_tools.subtract import subtract_first_image
subtract_first_image(ij, data, save=False, output_dir=""):

# Print dataset dimensions for X, Y, Z, TIME and CHANNEL
from ij2_tools.ij_utils import print_info

# Check if a point is inside a circle
from ij2_tools.geometry import in_circle
in_circle(point, center, radius)

# Return the points defining a circle
from ij2_tools.geometry import get_circle_points
get_circle_points(x_center, y_center, radius, n=20)

# Return the points defining the association of two circles
from ij2_tools.geometry import get_two_circles_points
get_two_circles_points(x1, y1, x2, y2, radius, n=20)

# Detect spots using the TrackMate DOG Detector
from ij2_tools.spot_detector import dog_detector
dog_detector(ij, data, radius, relative_threshold=1, doSubpixel=True, doMedian=False, calibration=None)

# Return the IJ1 ROI Manager
from ij2_tools.ij1 import get_roi_manager

Related links


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.