To view dataset

Hi,

I am new to this challenge and in dealing with this dataset. I downloaded the first zip file, but when I opened the .tif file all I had was just black images.

How should I view them properly, or is it even possible to view them? I am using a MacOS system.

Thank you in advance and apologize if it is a naive question.

Hi, Don't worry, thank you for this question and participating in Fuse My Cells!

As the images are 3D lightsheet microscopy images (i.e. fluorescence images), the background of the image is black ; despite our cuts, the first and last planes of the images often contain less information, hence the possible sensation of a black image.

You can use the (free) image processing software Fiji
https://imagej.net/software/fiji/downloads (available on Mac, Linux and Windows). Once installed, you can click and drop an image, then, moving around in the Z stack if you still don't see anything, go to Images, Adjust, Brightness/Contrast and click “Auto”.

You can see them with matplotlib as well (but only a single 2D plane). I used the skimage imread and for example the 150th plane shows some nucleus. For example you can test this (python) code:

from pathlib import Path
import matplotlib.pyplot as plt
from skimage.io import imread

fusemycells_db_path = Path("your_path")

img_0 = imread(fusemycells_db_path / "image_0_nucleus_fused.tif")
wanted_plane = int(img_0.shape[0]/2)
plt.imshow(img_0[wanted_plane, ...], cmap='gray')
plt.axis('off')
plt.show()

Let me know if you still have problems viewing the images.