(E2E-Export) .avi not exported properly + images darker

Hi There! First of all, thank you Mark for your work!

I was trying out your implementation for converting Heidelberg’s E2E format to images and videos, respectively. I can execute your example file with my exported E2E-file from HEYEX (v1) but there seem to be 2 problems:

1. The resulting .avi file seems to consist only of one image, although in the step where all slides get displayed through the volume.peek() code line, the images of the slides are all different.

2. The converted images of the slides seem to be a bit darker than what I see in the HEYEX software. Therefore, some areas of the slides are not displayed very detailed. However, I’m not sure how significant this problem is as I’m not an ophthalmologist nor do I have any kind of medical background.

Thanks for your help!

[Oli4]

I had a similar problem when working with the HEYEX VOL export, where I found the intensity transformation to be logarithmic. If the E2E data is the same as in the VOL file the following function might help:

def vol_intensity_transform(data):
    selection_0 = data == np.finfo(np.float32).max
    selection_data = data <= 1

    new = np.log(data[selection_data] + 2.44e-04)
    new = (new + 8.3) / 8.285

    data[selection_data] = new
    data[selection_0] = 0
    data = np.clip(data, 0, 1)
    return img_as_ubyte(data)

I found the output to differ by at most +/- 3 when compared with the XML export of the same volume for my small sample dataset. This difference arises from the same intensity in VOL data having multiple intensities in the XML data (See images below). There might be an additional context-sensitive processing step?

Plotted XML intensities(y-axis) againts VOL intensities (x-axis) Blue: intensities scatterplot (the values overlap) Red: function I use for the intensity transform

Zoom in on the plotted intensities.

If you are interested in reading the HEYEX VOL or XML export which do not seem to be supported by the OCT-converter, have a look at my package eyepy

[fabhari]

I had a similar problem when working with the HEYEX VOL export, where I found the intensity transformation to be logarithmic. If the E2E data is the same as in the VOL file the following function might help:

def vol_intensity_transform(data):
    selection_0 = data == np.finfo(np.float32).max
    selection_data = data <= 1

    new = np.log(data[selection_data] + 2.44e-04)
    new = (new + 8.3) / 8.285

    data[selection_data] = new
    data[selection_0] = 0
    data = np.clip(data, 0, 1)
    return img_as_ubyte(data)

I found the output to differ by at most +/- 3 when compared with the XML export of the same volume for my small sample dataset. This difference arises from the same intensity in VOL data having multiple intensities in the XML data (See images below). There might be an additional context-sensitive processing step?

Plotted XML intensities(y-axis) againts VOL intensities (x-axis) Blue: intensities scatterplot (the values overlap) Red: function I use for the intensity transform

Zoom in on the plotted intensities.

If you are interested in reading the HEYEX VOL or XML export which do not seem to be supported by the OCT-converter, have a look at my package eyepy

This helped me a lot thanks. the results are so promising