Resources
Our repositories
BEHAV3D: Dynamic immuno-organoid 3D imaging-transcriptomics platform to study tumor death dynamics and immune cell behavior.
BEHAV3D_Tumor_Profiler: Zero code computational framework for the comprehensive analysis of single tumor cell behaviors in live tissue and their interactions with the tumor microenvironment.
Behavioral-Guided-Transcriptomics: Analytical procedures required to integrate data from single-cell RNA sequencing of T cells with single-cell imaging data, providing for each sequenced cell probabilities of exhibiting different functional behaviors.
Below some user-friendly softwares for image segmentation and tracking and general data science resources for those starting to process (imaging) data.
FREE, USER-FRIENDLY PROTOCOLS for image processing
We understand that as a biologist, it can be challenging to access and fully utilize the cutting-edge tools developed by computational scientists. While many of these tools come with detailed descriptions, we've created simple, step-by-step guides to help you navigate some of the most advanced image processing tools with ease. Don’t forget to explore the other tools listed below as well!
Micro-SAM (μSAM) is a tool designed for interactive segmentation and tracking in microscopy images, built on top of the Segment Anything model. It enables accurate segmentation in 2D and 3D for diverse microscopy modalities, including light and electron microscopy. Through a Napari plugin, it provides both interactive and automatic segmentation, enhancing the efficiency and quality of image analysis across various microscopy tasks.
Microsam segmentation.pdfIlastik is an easy-to-use image analysis tool that uses machine learning to segment, classify, track, and count cells or other experimental data. You simply draw labels on the image, and the software learns from your input to classify pixels or objects. Most operations are interactive, allowing you to see results immediately, even on large datasets—no machine learning expertise required!
Ilastik.pdfOther free image processing tools incorporating machine learning tools
Understanding DEEP-LEARNING
Other sites of interest
Computational Biology and Bioinformatics Connection CSIC - Welcome card