markemus
markemus
This is a big problem- the process deletes the label image but not the macro image, which also has a copy of the label, at least on certain scanner settings.
- Updated to python3 and tested on the supported formats. - Added support for the Ventana TIF format specified by openslide here: https://openslide.org/formats/ventana/ - Wrapped the anonymization in a function...
I'm trying to load the DIR-lab 4DCT dataset, but I've run into some trouble. I downloaded the dataset from dir-lab.com, and applied the following pre-processing steps: > -downloaded all 10...
Hi @hsokooti I'm having trouble figuring out how to preprocess and load data into the net. I saw [your post](https://github.com/hsokooti/RegNet/issues/5#issuecomment-420634309) linking some datasets, but the model seems to load *.mha...
``` Traceback (most recent call last): File "/usr/lib/python3.5/runpy.py", line 184, in _run_module_as_main "__main__", mod_spec) File "/usr/lib/python3.5/runpy.py", line 85, in _run_code exec(code, run_globals) File "/home/markemus/dev/RegNet/RegNet3D.py", line 17, in import functions.RegNetModel as...
Hey, I just wanted to say thank you for your work putting this together, and to let you know that your code works perfectly on GPU with no modifications.
``` Traceback (most recent call last): File "/home/markemus/dev/pix2pix/stardist_imagej_script.py", line 52, in res = command.run(StarDist2D, False, "input", imp, "modelChoice", "Versatile (H&E nuclei)",).get() NameError: name 'command' is not defined ``` The script...
A few notes: - I wrote this for images scanned with Ventana's DP200 scanner. It assumes that images are in YCRCB format, which downsamples 2/3 color channels. We will need...
To replicate: ``` from libtiff import TIFFfile path = "/path/to/BigTIFF.tif" TIFFfile(path) ``` It says it's checking the magic number, but actually it's checking the version number. Bigtiffs have version number...
Hey @pearu, I wrote some code to allow pylibtiff to read 3D TIFF images. It's a modified version of the TIFF.read_tiles() method in libtiff_ctypes.py. Currently it's a monkeypatch that is...