Example page
Create Data/Dataset
Last modified: Nov. 11, 2024
Data Management Overview
Data Management is the core feature of I2S, where you can manage all of your image related data in one place. There are two major structures in this system: dataset and data. A dataset is a grouping of related image files, while data is a collection of datasets, typically from the same sample. For example, a data may contain two datasets, each dataset containing images taken under different conditions. A dataset can also be used as a container for files other than images.
Create Data
create data
From the sidebar, click Data, the Data List page will be displayed. Then click the Create Data button to create a new data.
Name: data's name (required).
Sample ID: If the data has an associated sample ID, you can input it here.
Tags: add tags to Data.
Created Date: the default created date is today. You can also change it to your preferred date.
Creator: the default creator is current user. You can also set the creator to any member in the company.
Add to Project: If you want to place the data in a project, you can select the project here. This can also be done after the data is created.
After filling in the fields, click the Create button, then the new data will be created.
Create Dataset
create_dataset
After the data is created, the data detail page will be shown. At the top right of the Datasets section, there is an Add Dataset button. When you click it, a new popup form will be shown to create a new dataset. The form has the following fields:
Dataset Name: The name of the dataset. The name must be unique in the data.
Image Type: The type of the dataset. The options are:
Images Stack: image stack. One or more 2D image files.
Raw: raw image. One .mhd file with a raw file.
Large 2D Image: a super large 2D image.
HDView: a super large 2D image in HDView format. One .zip file.
MRC Image: image in MRC format.
RLE: image in RLE format. One .am file.
DICOM Series: DICOM series images.
TXRM: ZEISS Xradia 3D image.
Labeled Image: check this option if the image is a labeled image.
Voxel Unit: choose the image's voxel unit.
Spacing: set the spacing between each voxel. Input 0 to use the image's original spacing or other values to overwrite the spacing. Use comma-separated values to input anisotropic spacing. e.g. 1.0, 2.0, 1.5
Highlight Color: choose your preferred background color for the dataset displayed in dataset table.
Upload Files to Dataset
upload image
After a new dataset is created, the dataset is empty. You need to upload your files to the dataset. Click the dataset row in the dataset table to show the dataset detail section. Click the upload icon to display the upload zone. You can drag your files into the zone or click it to select files.
Verify Dataset
After uploading your files to the dataset, the dataset's status is New. you need to verify the dataset to make sure it's a valid image. From the dataset table, find the dataset row, and click the verify dataset icon. A confirmation dialog will pop up to let you confirm, then click the Start button to start verifying the dataset. The dataset's status will be changed to "Verifying".
When the verification process is finished, the dataset status will be changed to its corresponding status. The status could be:
Valid: green background label with Grayscale if the image is grayscale or x Labels if the image is a labeled image.
NotImage: the system could not read this dataset as an image.
If the dataset is valid, then it is ready for image processing or simulation.