Using the Project Browser


Project Browser

The project browser is the widget that you will use to open files in Qi tissue.

New and Cached Datasets

When you open Qi tissue the project browser should be in the center of the screen, like this.

In the browser will be a list of cached files. If you are re-opening a dataset that you have used before, look through this list and double click the project you want to re-open. A white check will appear next to datasets with any cache saved, segmentation data stored, and all of its original data. The amount of cache allocated for each dataset is listed, as well as the date it was last opened (you can set an option in the preferences menu to clear any cache files for datasets that have not been opened for a specified amount of days, in order to clean up any excess storage. The default is set to 60).

If you are opening a dataset for the first time, click on the folder icon:

In the leftmost column will be a list of your folders. For efficiency, click "Set Dataset Root" and navigate to the place you keep your projects.

When you select a folder from the rightmost column, Qi will display all of the projects it finds in the folder in the right column. Select the project you want to open. If your images are divided into scenes, a third column will appear on the right with a list of scenes.
Select your scene and tissue and then double-click or select "Open" in the bottom left corner.

What is Cache?

Cache is a type of memory that is used to dramatically increase the speed of data access. Understanding how cache is written and stored is paramount when dealing with large amounts of cached image data, metadata, and processing pipelines.

First, let's understand the main difference between primary and secondary cache:

Primary cache is extremely fast, but limited in size, because it is normally built onto the processor chip using the system's RAM.

Secondary cache is external to the primary cache, located between the primary cache and the main memory.

Normally, the data required for any process resides in the main memory. However, it is allocated to the cache memory temporarily if it is used with enough frequency.

For example, if a process needs some data, it begins by searching in the cache memory. If it's available, QiTissue accesses the data as required. If no cache is pulled from, then the data is obtained from the main memory, which is then transferred to the cache memory under the assumption that it will be needed again.

So, cache memory is much faster than main memory, it can access the main memory in considerably less time (leading to faster execution of any process), and it can be removed from the cache and replaced by new data from the main memory. To achieve this level of speed, it can be computationally expensive. Understanding how to manage your cache is equally important.

Memory Management

If you navigate to Preferences from the file menu, you can set the primary cache location from your Systems Cache folder (the default) to a custom path, and manage additional your cache settings.

To prevent cache overload from happening, you may specify a primary cache size limit under "Total Max Cache Size", where no additional cache will generate if the specified amount is reached. However, the first hard check on your available disk space is the amount input in "Reserved Free Disk Space". If the disk fills up and reaches this limit, no more cache will be written, even before your total max cache size is reached. "Clean cache files older than" provides you with the ability to regularly purge cache that has not been opened for a designated time frame.

The "Clear All Cache" button will wipe all of the cache in the primary location, so be sure not to delete any relevant data by accident before selecting this.

QiTissue automatically creates a secondary cache folder that stores additional data, such as log files, locally changed biomarker entries, custom image or biomarker feature panels, etc.

You can quickly navigate to your primary cache folder by going to Memory Management in Preferences and clicking "Show in Finder".