Mesmerize Demo

The demo project contains a few samples from the Ciona project, and a few example analysis flowcharts, and an interactive zscore heatmap plot.

decompress using pigz:

pigz -dc demo_project.tar.gz | tar xf -

If you cannot install pigz use, tar, but it will be much slower:

tar xvzf demo_project.tar.gz

The demo project can be opened from the Mesmerize welcome window, the first window that appears when Mesmerize is launched.
http://mesmerizelab.org/user_guides/general/misc.html

After opening the project, the 3 project samples can be explored using the Project Browser
http://mesmerizelab.org/user_guides/project_organization/project_browser/project_browser.html
FlowchartsPlease see the following Flowchart docs:
http://www.mesmerizelab.org/user_guides/flowchart/overview.html
http://www.mesmerizelab.org/user_guides/flowchart/nodes.html
Each flowchart will take a few seconds to open as the data are loaded from disk. You can see the progress bar in the terminal that Mesmerize is running in.

hierarchical_clustering_freq_domain

Example illustrating hierarchical clustering using frequency domain data. Refer to their corresponding analysis graph in the "analysis_graphs" direcotry to verify the parameters for each node. To begin the process choose "_SPLICE_ARRAYS" as the data column for the "Linkage" node and click the "Apply" checkbox. Compute time was ~3 minutes on a 32 core AMD Ryzen CPU. You can visualize the output of the FCluster node using a heatmap.
http://www.mesmerizelab.org/user_guides/flowchart/nodes.html#heatmap

simple_peak_detection
Perform simple peak detection using derivatives. You will get a window stating that a few curves were excluded. Click "OK".
Docs for Peak Detect node: http://www.mesmerizelab.org/user_guides/flowchart/nodes.html#peakdetect
Peak detection GUI: http://www.mesmerizelab.org/user_guides/plots/peak_editor.html#plot-peakeditor

zscore_all_tagged
View a heatmap of all tagged data after z-scoring. Choose appropriate data & label columns for display with the heatmap. For example set "Data column" to "_ZSCORE" and "Labels column" to "cell_name" or "promoter".

Heatmap docs: http://www.mesmerizelab.org/user_guides/plots/heatmap.html
Batches for Caiman motion correction & CNMFETwo batches containing a motion correction & CNMFE item are available in the "batches" directory. These batches can be opened using the batch manager.
http://mesmerizelab.org/user_guides/viewer/modules/batch_manager.html

The input image sequence of each batch item can be viewed by clicking on the batch item of interest and clicking the "View Input" button. The outputs can be viewed by double cliking the batch item. The batch items can be processed by clicking the "Start" button. Each item takes ~5 minutes on an AMD Ryzen CPU with 16 cores.

You will need to setup the system configuration before running a batch item:
http://mesmerizelab.org/user_guides/general/misc.html#system-configuration

The batch items were created from the raw data using the Caiman Motion Correction & CNMFE modules in the Viewer.

http://mesmerizelab.org/user_guides/viewer/overview.html

http://mesmerizelab.org/user_guides/viewer/modules/caiman_motion_correction.html#module-caimanmotioncorrection

http://mesmerizelab.org/user_guides/viewer/modules/cnmfe.html