Anwai Archit issues

Results 34 issues of


                                            Anwai Archit

Sampling a Segmentation

Hi Stefan, thanks for this nice PyTorch implementation. I have a question regarding the `sample` function in the `probabilistic_unet.py` file. In line [222](https://github.com/stefanknegt/Probabilistic-Unet-Pytorch/blob/master/probabilistic_unet.py#L222) (while training), wouldn't we want to sample...

Scribble-based segmentation

This in particular could potentially be a nice feature to segment vessel-like thin (and long) structures using positive scribblles, or eliminate the outside-boundary region in-a-go for parts outside the object...

enhancement

`empanada` codebase not accessible

Hi @conradry, The [empanada](https://github.com/volume-em/empanada) scripts are not accesible on GitHub at the moment. Can you please have a look at what's happening there? (I would be interested to make use...

Update trainers to compute loss over low_res_mask

Update trainers to change the labels before one hot

Add masks to first iteration for iterative prompting

Scripts for finetuning for chromosome segmentation in EM

Hi @constantinpape, This is a finetuning script for Gunar, for finetuning micro-sam (`vit_b_em_organelles`) on their own data. I made a random split out of one unified dataset to avoid making...

Minor update to ignore warnings in train_sam functionality

Add out of domain test datasets for benchmarking finetuned models

The idea for this would be to have scripts unified in one place for evaluating automatic and interactive segmentation capabilities of `micro-sam` on a diverse set of open-source datasets (i.e....

Add dry run for loaders to check for valid instances

Takes care of https://github.com/computational-cell-analytics/micro-sam/issues/703