`pyimagej` provides functions for integration between ImageJ and Python. Questions about `pyimagej` are best asked on https://forum.image.sc, the primary channel for support of both ImageJ and pyimagej.
Questions tagged [pyimagej]
11 questions
1
vote
0 answers
Calling an ImageJ/FIJI macro from inside a jupyter notebook
I would like to use ImageJ and some of its macros and call them from inside a jupyter notebook. I am aware of PyimageJ, and I have been able to install it and load an image for display using ImageJ methods. But I am having some difficulties in…
Materia Dura
- 21
- 3
0
votes
2 answers
The error "pyimage1 doesn't exist" doesn't let me set background image
I want to put the image for background.My code follows..
import PIL
from PIL import ImageTk
from PIL import Image
import PIL.Image
class App(tk.Tk):
def __init__(self):
super().__init__()
self.withdraw()
self.root1 = Tk()…
pegah zahedi
- 15
- 4
0
votes
0 answers
Failed to create a JVM with the requested environment
I was trying to initialize imagej(imagej.init()) but this error comes everytime. I have tried everything but not able sort it out.
# Failed to bootstrap the artifact.
Possible solutions:
* Double check the endpoint for correctness…
Hivanshu Tyagi
- 1
- 2
0
votes
1 answer
open cv code crops an image 56 times and each cropped image has same metadata as original image
(I am new to this whole open cv thing)
My cropping method is to click a point on the image near the top left where you want the first box and the clicked point will be the starting coordinate for the rest of the cropping. (if there is an easier…
sara kim
- 1
0
votes
1 answer
JVM not running in Spyder 5.4.1 using PyImageJ
I am building a piece of software and trying to combine my analysis scripts between Spyder 5.4.1 (Python 3.8) and and ImageJ macros. My datasets are a series of .tif stack images, so I have decided to use PyImageJ to access the ImageJ2 gateway…
Eppicurt
- 173
- 10
0
votes
1 answer
is there any way to switch ImageJ macro code to python3 code?
I'm making an app in python3 and I want to use some function in imagej. I used macro recorder to switch to python code but it got really messy, now I don't know how to do next. Can someone help me, please.
Here is the marco recorder code and my…
Quân nguyễn
- 13
- 3
0
votes
2 answers
cannot install pyimagej on python
I need to write a code using jupyter notebook but need imagej packages.
I installed pyimagej using several commands
conda install -c conda-forge pyimagej
conda install -c conda-forge/label/cf201901 pyimagej
conda install -c…
Mohammed Zidane
- 3
- 3
0
votes
0 answers
Pyimagej conda install for use with JupyterLab Notebook, how do I resolve maven dependancy?
The installation using conda was straight forward with no errors. There was an extra step not mentioned in the installation guide to add the newly created pyimagej environment binary path to $PATH so Jupyterlab could find it. But then in testing…
Linda Marsh
- 105
- 1
- 1
- 9
0
votes
1 answer
Access FileSaver from pyimagej
How can one access FileSaver from pyimagej?
Everything that I see online is something like this:
from ij.io import FileSaver
But with pyimagej we are loading it differently:
import imagej
ij = imagej.init()
Also ij.io().FileSaver does not…
Oren
- 4,711
- 4
- 37
- 63
0
votes
1 answer
How do I plot a histogram's image from Pyimagej?
# Create an ImageJ gateway with the newest available version of ImageJ.
import imagej
import pathlib
import numpy
ij = imagej.init()
# Load an image.
img_path = pathlib.Path('C:/Users/Bernardo/TCC/thyroid/1_1.jpg')
image =…
Bernardo Cecchetto
- 71
- 6
0
votes
0 answers
Problems with pyimagej module imagej not found
I installed pyimagej:
pip3 install pyimagej
After installing it, I created a conda imagej environment.
conda create -n imagej -c conda-forge openjdk=8 pyimagej
In my pycharm IDE I set the right python interpreter in my imagej environment.
My…
Lisa B.
- 235
- 1
- 11