Page Comparison

...

...

Interface And Workflow

Aivia Cloud interface is shown below.

Image Removed

The Local Library box shows the content of the local computer folder linked to Aivia Cloud. You can adjust this setting by clicking on the Add Local Folder icon. The Cloud Library box shows the content of your folder in the Cloud. You can populate this folder by adding the chosen images from the Local Library to the Cloud Library. There are two ways to move the files between the Libraries  - using Move Selected to Cloud/Local buttons and drag & drop.

The right hand side panel gives you the access to the cloud computed processes. To set up a new job, use the Create Job tab. To monitor the job progress, use the Progress Queue tab.

Training a Deep Learning model

The (minimum of two) pairs of images used to create your own Deep Learning model (Deep Learning Training) should be distributed between the Raw Input box and the Example box. To introduce a new pair of images to the new job, move your original image from the Cloud Library to the Raw Input box and do similar with your analyzed image - move it from the Cloud Library to the Example box. To move files you can right click on your image to chose the correct option, or drag and drop.

Image Removed

The pairs of images used for Teaching get annotated with a corresponding green number on the top left of the thumbnail (see the Aivia Cloud Interface picture). Please, make sure that your pairs are matching correctly before running the job.

The Training Progress Queue informs you about the progress of your cloud computed job. Uploading indicates the process of moving a file from the local computer to the cloud. Having your files in the Cloud Library reassures this part of the job is instant. Allocating indicates the process of distributing the job tasks to the virtually unlimited CPU and GPU hardware of the cloud. Training shows your Deep Learning model training progress. You can monitor the progress updates by clicking on the Status button. The Training Status provides you with real - time plots of the training accuracy as the job progresses.

Image Removed

The Training results are saved to the new folder in your Cloud Library. The folder name starts with "Training" and contains two copies of the same Deep Learning model file saved in two different formats: .hdf5e and .pbe.

Image Removed

Teaching files

Aivia Cloud creating your own deep learning model starts with two (sets of) images - raw data and example data (aka ground truth).

For image segmentation tasks the ground truth data is composed of your annotations which can be created using one of Aivia's image analysis recipes, using one of the intelligent semi-automatic tools in Aivia or can be imported from other software tools. The raw data are the images as they were acquired by the microscope.

For restoration tasks the ground truth data is a set of data which represents the absolute best quality images (for that set up/experiment) that can be generated. The raw data is composed of images created using imaging parameters which are very desirable (e.g. very low laser power or very fast acquisition) but that can only generate sub-par images.

For prediction tasks the ground truth data is often a set of images which show the localization of a fluorescently tagged protein or organelle. The raw data is often composed of images created using a different imaging modality (e.g. bright-field) which the user wishes to use more routinely for any number of reasons (e.g. cost, photo-toxicity, fluorescence labeling complexity)

Deep Learning model types

Aivia Cloud provides pre-trained Deep Learning models and supports custom creation of six types of Deep Learning models:

• 2D/3D image segmentation model
• 2D/3D image restoration model
• 2D/3D image prediction model

By checking the "Transfer Learning" box you can join the existing model of choice with the newly learned data.

Applying a Deep Learning model

Using Aivia Cloud

Aivia Cloud creating your own deep learning model starts with two (sets of) images - raw data and example data (aka ground truth).

For image segmentation tasks the ground truth data is composed of your annotations which can be created using one of Aivia's image analysis recipes, using one of the intelligent semi-automatic tools in Aivia or can be imported from other software tools. The raw data are the images as they were acquired by the microscope.

For restoration tasks the ground truth data is a set of data which represents the absolute best quality images (for that set up/experiment) that can be generated. The raw data is composed of images created using imaging parameters which are very desirable (e.g. very low laser power or very fast acquisition) but that can only generate sub-par images.

For prediction tasks the ground truth data is often a set of images which show the localization of a fluorescently tagged protein or organelle. The raw data is often composed of images created using a different imaging modality (e.g. bright-field) which the user wishes to use more routinely for any number of reasons (e.g. cost, photo-toxicity, fluorescence labeling complexity)

Ground Truth Generation

Aivia Cloud 

Important Information

...