Bioimage informatics

Set of KNIME workflows for the training of a deep learning model for image-classification with custom images and classes.

The workflows take ground-truth category annotations as a table generated by the qualitative annotations plugins in Fiji.

Workflows for the training of a model AND for the prediction of image-category for new images are provided.

There are different workflows if you do:

- binary image-classification (images get classified in 1 category out of 2 possible categories) 

- classification from possibly more than 2 categories (images are classified in 1 category out of N possible categories).

The training workflows take care of image pre-processing and allows the visualization of the training and validation losses in real time along the training.  

For the training, transfer learning from a pre-trained VGG16 base is performed, with freshly initialized fully connected layers.

Only the fully connected layers are trained, the VGG16 base is frozen is this workflow, but once the fully connected layers trained the base could also be finetuned. In practice, it often works well with the frozen base.

Set of Fiji plugins facilitating the systematic manual annotation of images or image-regions. From a list of user-defined keywords, these plugins generate an easy-to-use graphical interface with buttons or checkboxes for the assignment of single or multiple pre-defined categories to full images or individual regions of interest. In addition to qualitative annotations, any quantitative measurement from the standard Fiji options can also be automatically reported. Besides the interactive user interface, keyboard shortcuts are available to speed-up the annotation process for larger datasets.

The plugins can be installed by activating the Qualitative annotations update site in Fiji.

This macro toolset offers additional click tools for the rapid annotations of ROI in ImageJ/Fiji.

The ROI 1-click tools can be setup with a predefined shape, and custom actions to perform upon click (Add to ROI Manager, Run Measure, Go to next slice, run a macro command...)

To install in Fiji, just activate the ROI 1-click tools 

ImageM integrates into a GUI several algorithms for interactive image processing and analysis. Interface is largely inspired from the open source software "ImageJ".

This tool allows the user to define structures of interest by interactively marking a subset of pixels. Thanks to the real-time feedback, the user can place new markings strategically, depending on the current outcome.