From dce0628df822f8f37ccf293b010e91f699cde3aa Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Efe=20=C3=87iftci?= Date: Sun, 15 Dec 2024 15:20:08 +0300 Subject: [PATCH] Update README.md --- README.md | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/README.md b/README.md index 7a58b17..8250bf6 100644 --- a/README.md +++ b/README.md @@ -57,7 +57,7 @@ MitoSeg can be compiled with: | `--thick ` | Specifies the snake z-thickness. The given value must be between 5 and 500 (default: 20). Can be set to `full` to use the whole z-range specified by the `--zrange` argument. Snake thickness affects the segmentation accuracy; thicker snakes provide continuous smooth segmentation along the z-range, but can also produce more false negatives. | | `--phase ` | Specifies a specific phase to be executed (1, 2, or 3). The `--valid` and `--thick` arguments affect the 2nd and 3rd phases, respectively. Hence, if the same portion of the dataset is to be segmented by changing only these arguments, the `--phase` argument can be used to restart a particular phase to avoid redundant computation manually. If not used, MitoSeg will execute all phases in order. | | `--cores` | Specifies the number of CPU cores that work in collaboration to speed up the process. | -| `--settings-file ` | Specifies the path of a YAML file containing custom segmentation variables. | +| `--settings-file ` | Specifies the path of a YAML file containing custom segmentation variables. Details can be found [here](https://github.com/fstasel/mitoseg/wiki/Setting-file-description). | ## Examples @@ -77,6 +77,8 @@ MitoSeg can be compiled with: ## Launching Graphical User Interface MitoSeg also includes a simple graphical user interface (GUI) developed using the Python Tkinter library. After building MitoSeg, the GUI can be launched by executing `mitoseg-gui.py` from the build directory. +![mitoseg_screenshot](https://github.com/user-attachments/assets/8bc3726f-cbe8-420b-8075-69504537a38c) + ## Running MitoSeg as a Docker Application MitoSeg can also be used within a [Docker](https://www.docker.com/) environment, which eliminates the need to prepare the building environment on your computer, and allows MitoSeg to run on various operating systems easily. A sample Dockerfile is provided under the `docker` directory, which can be used for building a Docker image by executing the following command within the `docker` directory: