New data added !! - 16/01/2025

Hello everyone,

Thank you for participating in Fuse My Cells!

We added new data in the database. Be careful about the Z degradation (ascending / descending) and some new images has no Z degradation but X(Y) degradation.

PS: Do not hesitate to ask questions, to share information and to inform us of any problem.

I might be wrong but, although you say

we have updated all the images with a few z-plane crops to reduce the empty/black parts of the images. This changes the 3D sizes, which are no longer standard (and reduces the final file size, lightening the final size of the database)

I seem to see empty/black part of images in most of the images I downloaded. For example, image_4_nucleus_angle.tif and image_4_nucleus_fused.tif are both empty on Z-slices 0-25 and 203-230.

Apologies if that's a misunderstanding from my end.

Thank you for your message,

I checked this image and I understand what's going on. When cropping the images, I set a threshold of 150 pixels (instead of 0 after checking various images). So, I only deleted shots that didn't contain pixels larger than 150 px.

As it happens, there are certain areas of the shots that have “little artifacts” of light, so these shots were not considered “ full black ”. This is what happens in image_4_nucleus_fused.tif (and maybe some few others).

I see, it makes total sense, thanks for clarifying, I was just afraid I was displaying images wrong / not understanding the data well, I'm reassured now :)

Is it normal to have almost completely dark images for slices in the middle? E.g. image 181 nucleus (fused, so supposedly ground truth) have clear images with relevant information for low Z and high Z but for Z = 444 for example, there is nothing.

Minimal Reproducible Example:

import matplotlib.pyplot as plt
import tifffile

file_path_fused = "data/image_181_nucleus_fused.tif"
image_3d_fused = tifffile.imread(file_path_fused)
plt.imshow(image_3d_fused[444, :, :], cmap='gray', vmin=0, vmax=image_3d_fused.max())
plt.axis('off')
plt.show()