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The JP2 files open in a IIIF viewer and provide excellent Pan-Zoom capabilities, like the slideshow below illustrates. The new files then automatically populate along with their records and now remain either public or non-public according to their original setting.

#Enhance zoomify full

In other cases, where there was no PDF, I would open an alternate JPG file for Full and Detail images and simply used the standard “Replace” button for the Full or Details file.

#Enhance zoomify pdf

In some cases, I could open the PDF file associated with pages and save them as JP2 – although these tend to be quite large, so we adjusted the quality during the conversion process to reduce the storage overhead.When certain Zoomify files were identified as too corrupt and this simpler workflow did not work, a workaround was created:.In the data management side of the VITA toolkit, I then activated a task-specific button to replace the broken Zoomify files with newer (and unbroken) JP2 image files.

#Enhance zoomify software

I used Irfanview software to convert JPG files to JP2 files, and I assigned their original file names so that the agencies could trace the display files back to their master copies.

“Dezoomify” merges the tiles that make up a Zoomify file and that merged image can then be saved as a JPG.

Using the Dezoomify tool which works by copying and pasting the item’s public URL into the tool.

Using a RecordID list that was organized by Agency, I could identify all of the records with images that needed to be replaced and re-loaded. This was done for Full images, some Details and Reverse images, as well as for many book and scrapbook pages. My primary task was to open and convert the broken Zoomify files and then replace them with JP2 files. ODW provided me with a list that identified records with broken Zoomify files and I got started on the clean-up-work! In my time at ODW, I have worked on (and completed) the Dezoomify project which primarily involved using the VITA Toolkit to access and replace collection images and other software for the conversion process. We were lucky to have Christine Anderson, a Mohawk College Library Technician student, who was willing and able to take on the task.

#Enhance zoomify manual

We were able to do this systematically for the most part, but some stubborn items required manual intervention and conversion. The trick was that we needed to go through our system and replace the old Zoomify folders with JP2 files. So, any user uploading full images, details, or pages can upload the considerably lighter and mobile-friendly JP2 file and it displays with all the pan, zoom and rotate options people expect for viewing this kind of material online. Luckily, as technology has advanced and streamlined, the standard is now to use JPEG-2000 (JP2) files that automatically trigger the open-source IIIF (International Image Interoperable Framework)viewer in VITA. Java is ran in a headless mode when the application does not interact with a user (if not specified, the default is =false) If you are not sure how much memory your system has, run the command free -h and check the value under total. The flag Xmx specifies the maximum memory allocation pool for a Java virtual machine, from our experience 48000m works well when processing human data sets.

pairs file that you generated in the From fastq to final valid pairs bam file section can be used directly with Juicer tools to generate the HiC contact matrix: Stores contact matrix at 9 different resolutions (2.5M, 1M, 500K, 250K, 100K, 50K, 25K, 10K, and 5K)Ĭan be programmatically manipulated using straw python API Provides rapid random access to any genomic region matrix

HiC is highly compressed binary representation of the contact matrix