Reviewer response for version 1
In this manuscript authors presented a computational tool that extracts text and images from PDF files. 
In general the manuscript is interesting considering that it can analyze various types of PDF files from different scientific areas based on the keywords and coordinates. 
However, it lacks technical novelty over the published literatures and needs additional input on the image analysis section before indexing.
Extraction of texts and images from scientific publications has been presented in various domains: computer science 1 , biomedical 2 - 4 , chemistry 5 , proteomics 6 and so on. 
The manuscript by Zeeshan Ahmed and Thomas Dandekar presents an incremental innovation without providing clear technological advancement in the field. 
The objective of performing both physical and logical structure analysis of all kinds of PDF files as mentioned in the manuscript has not been sufficiently supported by technological contribution described in Methods section.
The image processing section the manuscript has been very brief. 
It does not provide any advanced image analysis technique as mentioned in the abstract. 
Authors should mention how exactly segmentation of figures and labels are performed and how they are represented to make logical connection between different entities in order to perform further analysis and customized visualization.
The framework has been tested with a very small set of PDF files and no qualitative/quantitative result reporting the accuracy with respect to manually annotated files was presented. 
It would be good to increase the number test files and include the results of qualitative/quantitative analysis.
Some of the figures (Figures 1, 3, 4 and 6) in the manuscript are hard to see the details in both online and print format. 
These figures could be reformatted.
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