How can I display an image from a file in Jupyter Notebook?

Question

I would like to use an IPython notebook as a way to interactively analyze some genome charts I am making with Biopython\'s GenomeDiagram module. While there is extensive doc

Answer 1

You could use in html code in markdown section: example:

 <img src="https://www.tensorflow.org/images/colab_logo_32px.png" />

Answer 2

If you want to efficiently display big number of images I recommend using IPyPlot package

import ipyplot

ipyplot.plot_images(images_array, max_images=20, img_width=150)

There are some other useful functions in that package where you can display images in interactive tabs (separate tab for each label/class) which is very helpful for all the ML classification tasks.

Answer 3

A cleaner Python3 version that use standard numpy, matplotlib and PIL. Merging the answer for opening from URL.

import matplotlib.pyplot as plt
from PIL import Image
import numpy as np

pil_im = Image.open('image.png') #Take jpg + png
## Uncomment to open from URL
#import requests
#r = requests.get('https://www.vegvesen.no/public/webkamera/kamera?id=131206')
#pil_im = Image.open(BytesIO(r.content))
im_array = np.asarray(pil_im)
plt.imshow(im_array)
plt.show()

Answer 4

When using GenomeDiagram with Jupyter (iPython), the easiest way to display images is by converting the GenomeDiagram to a PNG image. This can be wrapped using an IPython.display.Image object to make it display in the notebook.

from Bio.Graphics import GenomeDiagram
from Bio.SeqFeature import SeqFeature, FeatureLocation
from IPython.display import display, Image
gd_diagram = GenomeDiagram.Diagram("Test diagram")
gd_track_for_features = gd_diagram.new_track(1, name="Annotated Features")
gd_feature_set = gd_track_for_features.new_set()
gd_feature_set.add_feature(SeqFeature(FeatureLocation(25, 75), strand=+1))
gd_diagram.draw(format="linear", orientation="landscape", pagesize='A4',
                fragments=1, start=0, end=100)
Image(gd_diagram.write_to_string("PNG"))

[See Notebook]

Answer 5

from IPython.display import Image

Image(filename =r'C:\user\path')

I've seen some solutions and some wont work because of the raw directory, when adding codes like the one above, just remember to add 'r' before the directory. this should avoid this kind of error: (unicode error) 'unicodeescape' codec can't decode bytes in position 2-3: truncated \UXXXXXXXX escape