docu update and new logo image

Author: petersenpeter

docs/index.md

@@ -44,7 +44,7 @@ mex -O CCGHeart.c
 5. That's it! Now you can explore the software with below example data or try one of the tutorials.
 
 ### Try the Cell Explorer with example data
-There is an example dataset included in the repository for trying the Cell Explorer. Load the mat-file [`cell_metrics_batch.mat`](https://github.com/petersenpeter/Cell-Explorer/blob/master/LoadCellMetricBatch.m) into Matlab and type:
+There is an example dataset included in the repository for trying the Cell Explorer. Load the mat-file [`cell_metrics_batch.mat`](https://github.com/petersenpeter/Cell-Explorer/blob/master/LoadCellMetricsBatch.m) into Matlab and type:
 ```m
 CellExplorer('metrics',cell_metrics)
 ```

docs/pipeline/running-pipeline.md

@@ -28,7 +28,7 @@ Following the definition of metadata, the cell metrics calculation process can b
 ![](https://buzsakilab.com/wp/wp-content/uploads/2020/03/FlowChart_pipeline.png)
 
 ### Running Cell Explorer
-The Cell Explorer can be used to display single cell_metrics files as well as batches. Batch loading is performed with the script LoadCellMetricBatch. The advanced flowchart below further details the capabilities of loading various GUIs from the Cell Explorer (gui_session, gui_MonoSyn and gui_DeelSuperficial) as well as do spike raster plots, that requires access to the local spikes struct and potentially also manipulation and events files if plotting PSTHs.
+The Cell Explorer can be used to display single cell_metrics files as well as batches. Batch loading is performed with the script LoadCellMetricsBatch. The advanced flowchart below further details the capabilities of loading various GUIs from the Cell Explorer (gui_session, gui_MonoSyn and gui_DeelSuperficial) as well as do spike raster plots, that requires access to the local spikes struct and potentially also manipulation and events files if plotting PSTHs.
 ![](https://buzsakilab.com/wp/wp-content/uploads/2020/03/FlowChart_CellExplorer.png)
 
 ## Running pipeline from a data path
@@ -46,11 +46,11 @@ session = gui_session(session);
 
 To run the pipeline from the Matlab Command Window from the session struct type:
 ```m
-cell_metrics = calc_CellMetrics('session', session);
+cell_metrics = ProcessCellMetrics('session', session);
 ```
 You can also run it directly from a basepath and generate the session struct directly:
 ```m
-cell_metrics = calc_CellMetrics;
+cell_metrics = ProcessCellMetrics;
 ```
 When calling the pipeline with the sessionTemplate, a GUI will be shown allowing you to edit the metadata both for the input parameters and the session struct. 
 
@@ -63,15 +63,15 @@ To open multiple sessions together you can run the Cell Explorer in batch mode.
 
 ```m
 bsasepaths = {'sessionName1','sessionName2','sessionName3'};
-cell_metrics = LoadCellMetricBatch('basepaths',bsasepaths);
+cell_metrics = LoadCellMetricsBatch('basepaths',bsasepaths);
 cell_metrics = CellExplorer('metrics',cell_metrics);
 ```
 As you perform classifications in the Cell Explorer, you may save back to the original cell metrics stored with the sessions defined above. You can perform the batch mode from a list of paths as well.
 
 ## Running pipeline using the Buzsaki lab database
 The Cell Explorer pipeline uses a single Matlab struct for handling metadata. The struct is automatically loaded from the buzsaki lab database if you are running the pipeline with the database, and is located in the base path once a session has been processed. To run the pipeline on a session named 'PetersSession' using the database type:
 ```m
-cell_metrics = calc_CellMetrics('sessionName','PetersSession');
+cell_metrics = ProcessCellMetrics('sessionName','PetersSession');
 ```
 To view the result in the Cell Explorer type:
 ```m
@@ -82,7 +82,7 @@ To open multiple sessions together you can run the Cell Explorer in batch mode.
 
 ```m
 sessionNames = {'sessionName1','sessionName2','sessionName3'};
-cell_metrics = LoadCellMetricBatch('sessions',sessionNames);
+cell_metrics = LoadCellMetricsBatch('sessions',sessionNames);
 cell_metrics = CellExplorer('metrics',cell_metrics);
 ```
 As you perform classifications in the Cell Explorer, you may save back to the original cell metrics stored with the sessions defined above. You can perform the batch mode from a list of paths as well.

docs/tutorials/database-tutorial.md

@@ -45,7 +45,7 @@ spikes = loadSpikes('session',session);
 7. Loading via database/metadata
    1. Run the processing pipeline and CellExplorer from `sessionName`
 ```m
-cell_metrics = calc_CellMetrics('sessionName',sessionName);
+cell_metrics = ProcessCellMetrics('sessionName',sessionName);
 cell_metrics = CellExplorer('metrics',cell_metrics);
 ```
    1. Run Cell Explorer directly from `sessionName`
@@ -55,7 +55,7 @@ cell_metrics = CellExplorer('sessionName',sessionName);
    1. Run Cell Explorer from list of `sessionNames`
 ```m
 sessionNames = {'ham11_27-29_amp','ham11_34-36_amp'};
-cell_metrics = LoadCellMetricBatch('sessions',sessionNames);
+cell_metrics = LoadCellMetricsBatch('sessions',sessionNames);
 cell_metrics = CellExplorer('metrics',cell_metrics);
 ```
 

docs/tutorials/general-tutorial.md

@@ -17,9 +17,9 @@ cd(basepath)
 ```m
 session = sessionTemplate(basepath,'showGUI',true);
 ```
-3. Run the cell metrics pipeline `calc_CellMetrics` using the session struct as input
+3. Run the cell metrics pipeline `ProcessCellMetrics` using the session struct as input
 ```m
-cell_metrics = calc_CellMetrics('session', session);
+cell_metrics = ProcessCellMetrics('session', session);
 ```
 4. Visualize the cell metrics in the Cell Explorer
 ```m
@@ -29,7 +29,7 @@ cell_metrics = CellExplorer('metrics',cell_metrics);
 ```m
 basenames = {'Rat08-20130708','Rat08-20130709'};
 clusteringpaths = {'/Volumes/buzsakilab/Buzsakilabspace/Datasets/GirardeauG/Rat08/Rat08-20130708','/Volumes/buzsakilab/Buzsakilabspace/Datasets/GirardeauG/Rat08/Rat08-20130709'};
-cell_metrics = LoadCellMetricBatch('clusteringpaths',clusteringpaths,'basenames',basenames);
+cell_metrics = LoadCellMetricsBatch('clusteringpaths',clusteringpaths,'basenames',basenames);
 cell_metrics = CellExplorer('metrics',cell_metrics);
 ```