Load .gif and retrieve physical dimensions-CodePudding

The

gif source

One could do the following to get the frames in GIF.(code ref.)

from PIL import Image, ImageSequence img = Image.open(filename) frames = [] for frame in ImageSequence.Iterator(img): a = np.array(frame.convert('RGB').getdata(), dtype=np.uint8) a = a.reshape(frame.size[1], frame.size[0],3) frames.append(Picture(a)) return frames

I am not sure what has to be done next.

Could someone please offer some suggestions?

CodePudding user response：

To put it simply you can NOT find the exact volume occupied by each cell in the 3D volume. It is impossible without the 3D object raw data. (just one example of this that there are multiple cells inside the object that you cant see clearly with human eye, so you cant get their data from a picture)

You maybe able to make a complicated algorithm that can get a rough estimation of the volume of the whole object, but it will be very difficult and the accuracy will be low, because there are multiple factors (for example you cant predect if the object is hollow or if it has holes inside it)

CodePudding user response：

As Jabbar mentions, you won't be able to get an exact value, but with some computer vision processing, you should be able to get the voxel dimensions, and if you know the scale of the image, you should be able to scale that value to a physical volume.

First you need to run edge detection and some kind of blob detection to get the individual cells.

Generate a segmentation label for each slice. This is a 2D uint32 array which has a unique number for each entity (cell) you want the volume of.

With your per-layer segmentation labels, you need to correlate the label IDs of the same cell across multiple slices. This will probably be the hardest part, but it's probably ok if it isn't perfect.

Once you have a segmentation mask for each cell in each frame, you can generate a 3D segmentation mask - a 3D array for each cell, which is a boolean mask (True where the cell volume is, False elsewhere)

Sum that array to get the volume (in voxels) of the cell

Scale your voxel volume by the ratio of pixel width and slice depth to physical distance.