Semi-automated

This plugin allows to compute a similarity (translation/rotation/scaling and flipping) transform from pair of points. It is updating the transformed image interactively such that the user get immediate feedback. The transformation is saved and can be applied to any other stack/image. Non rigid deformation can also be applied in 2D or 3D.

3D/3D,2D/3D or 3D /2D can be handled .

3D ROI are enabled, and can be checked with the 3D vtk view (size of ROI can be changed using the ROI stroke width).

Some prealignment by rotating in 3D the volume is possible.

Transformations can be applied directly or combined through Block Protocols (search for apply transformation).

It's also provide information about the predicted Error (based on statistical prediction), either as a full color mapping, either on each points used as landmarks, and error on the discrepancy in position between points.

There are video tutorials available in the web.

The jicbioimage Python package makes it easy to explore microscopy data in a programmatic fashion (python).

Exploring images via coding means that the exploratory work becomes recorded and reproducible.

Furthermore, it makes it easier to convert the exploratory work into (semi) automated analysis work flows.

Features:

• Built in functionality for working with microscopy data
• Automatic generation of audit trails
• Python integration Works with Python 2.7, 3.3 and 3.4

TurtleSeg is an interactive 3D image segmentation tool. TurtleSeg has an automated system, Spotlight, for automatically directing the user towards the next steps. Typically, a user loads a 3D image and then manually contour a sparse number of slices, the full 3D segmentation can then be built automatically.

XuvTools (pronounced “ex-you-vee-tools”) is a fully automated 3D stitching software for biomedical image data, typically confocal microscopy images. XuvTools runs on Microsoft Windows XP and Vista, Linux and Apple Mac computers. It supports 32 and 64bit operating systems (with 64bit highly preferred). XuvTools is free and open source software (see Licensing), so you can start using it immediately. Go to Downloads and give it a try. The goal of XuvTools is to provide tools, that combine multiple microscopic recordings to obtain a larger field of view (“stitching”) and a higher dynamic range (“HDR” recombination), or better resolution (multi view reconstruction), and to make these tools publicly available.

The MorphoLeaf application allows you to extract the contour of multiple leaf images and identify their biologically-relevant landmarks. These landmarks are then used to quantify morphological parameters of individual leaves and to reconstruct average leaf shapes. MorphoLeaf is developed by the Modeling and Digital Imaging and the Transcription Factors and Architecture teams of the Institut Jean-Pierre Bourgin, INRA Versailles, France, and the Biophyscis and Development group at RDP, Lyon.