cerberus

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ajinkya-kulkarni

model training

2

I greatly appreciate your work and hope that you can release your training code. Thanks a lot.

zymissy

Hi. I found a bug while trying to run_infer_wsi.py . When using msk_file, the inst_info["box"] is returning the wrong coordinates. [Here](https://github.com/TissueImageAnalytics/cerberus/blob/5bcecbb071bebd5911250034c94f3568f23f50bb/infer/wsi.py#L816)(816 line at /infer /wsi.py), if you add tissue_topleft ([cmin,...

YOOHYOJEONG

Possible to finetune the model on custom dataset(s)

1

Hello team, thanks for this repo! I have a short question - is it possible to finetune the model on custom dataset(s)? For example, if I have a custom annotated...

ajinkya-kulkarni

environment.yml inonsistency

1

Conda gives me this ``` The conflict is caused by: The user requested openslide-python==1.1.2 tiatoolbox 1.3.1 depends on openslide-python>=1.2.0 ```

curlup

output labels

4

In the mat file, the predicted tissue class in pclass_mat or cell type in nuclei_mat are stored as integer. I could not find how to map those integers to actual...

anooyih

The bug is: ```shell (cerberus) huangdenan@Cypresss-MacBook-Air cerberus-master % ./run_tile.sh Usage: run_infer_tile.py [--gpu=] [--model=] [--nr_inference_workers=] [--nr_post_proc_workers=] [--batch_size=] [--input_dir=] [--output_dir=] [--patch_input_shape=] [--patch_output_shape=] run_infer_tile.py (-h | --help) run_infer_tile.py --version ./run_tile.sh: line 5: --model=/root/romesco_workspace/resnet34_cerberus:...

CarlCypress

Getting the same error as in https://github.com/TissueImageAnalytics/cerberus/issues/26 Cant create the environment because of various conflicts: (Truncated log) ``` Package python conflicts for: progress==1.5=py37h06a4308_0 -> python[version='>=3.7,=3.5.1,=2.7,=3.10,=3.9,=3.8,=3.12.0rc3,=3.11,=3.6,=3.5,=3.13,=3.12,=3.13.0rc1,=3.7,=1.16.6,=2.7,=3.10,=3.11,=3.12,=3.9,=3.12.0rc3,=3.8,=3.6,=3.7'] shapely==1.7.1=py37h1728cc4_0 -> python[version='>=3.7,=3.7,=3.7,=3.7,=2.48.0'] -> python[version='*|>=2.7|>=3.6,=3.7,=3.8,=2.7,=3.7,=3.7,=3.7,=2.3.0,=2.7,=3.10,=3.11,=3.9,=3.12,=3.13,=3.13.0rc2,=3.13.0rc1,=3.8,=3.6,=3.7,=2.3.0,=2.7,=3.10,=3.11,=3.9,=3.12,=3.13,=3.13.0rc2,=3.13.0rc1,=3.8,=3.6,=3.5,=3.7,=3.7,=3.7,=3.7,=2.7,=3.10,=3.7|>=3.8|>=3.9|>=3.9,=3.8,=3.11,=3.6,=3.5,=3.13,=3.12,=3.6']...

Himanshunitrr