4D (space + time) datasets of spruce wood enzymatic hydrolysis

TL;DR

This paper presents 4D datasets of spruce wood cell walls during enzymatic hydrolysis, enabling detailed analysis of the process over time.

Contribution

The study introduces time-lapse image datasets and a novel image processing pipeline for tracking cell wall hydrolysis in spruce wood.

Findings

AIMTrack efficiently processes time-lapse images by dynamically adjusting cluster sizes to correct sample drift.

The datasets include enzymatic hydrolysis of spruce wood at two enzyme loadings and corresponding control datasets.

Segmentation of cell walls is achieved with unique identifiers for tracking over time.

Abstract

The conversion of lignocellulosic biomass from plant cell walls into bioproducts can contribute to reducing dependence on fossil sources and achieving sustainable development. Biotechnological conversion of lignocellulosic biomass has several advantages over other conversion approaches such as thermochemical and chemical conversions. These advantages include improved efficiency and specificity for desired products, ecological compatibility and reduced toxicity. Enzymatic transformation is a key step in biotechnological conversion. To achieve a cost-effective conversion, a comprehensive understanding of cell wall enzymatic hydrolysis is required. Despite progress, the enzymatic hydrolysis at microscale is comparatively understudied and lacks comprehensive investigation. Addressing this gap requires collection of time-lapse image datasets of cell wall enzymatic hydrolysis which is a technically demanding task. Furthermore, accurate processing of the time-lapse images to identify and track individual cell walls is particularly challenging, notably because of the sample drift present in the images. Recently, an efficient image processing pipeline, called AIMTrack, has been developed which uses an enhanced divide-and-conquer strategy to divide time-lapse images into clusters whose sizes are dynamically adjusted to the deconstruction extent. The image registrations are then limited to clusters and the resulting transformations are combined to correct sample drift across time-lapse images. Subsequently AIMTrack provides segmentation of time-lapse images where voxels belonging to the same cell walls are labelled with a unique identifier. The time-lapse image datasets presented here consist of time-lapse images of spruce wood cell walls acquired during enzymatic hydrolysis using a cellulolytic enzyme cocktail at two enzyme loadings of 15 and 30 FPU/g biomass. Control time-lapse datasets which are acquired under the identical conditions, but without addition of enzymes, are also included. Both control and hydrolysis datasets are processed using AIMTrack to track the cell walls from time-lapse images. The generated segmentations are also provided.

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