Project Setup

The Project tab is the first configuration step. It holds metadata about your experiment and controls how images are loaded and grouped.

Experiment Metadata

Field	Description
First / Last name	Experimenter name stored with the project file
Organization	Institution or lab name
Experiment name	Human-readable label for this experiment
Notes	Free-text notes

Image Directory

Set Image directory to the root folder containing your microscopy images. EVAnalyzer performs a recursive search and lists every supported file under that folder in the Images tab.

Job Name

The Job name identifies this particular analysis run. Results are stored under:

<image_directory>/evanalyzer/<job_name>/

If left blank, EVAnalyzer auto-generates a name from the current timestamp.

Image Grouping {#image-grouping}

Grouping controls how images are aggregated in the results view.

Mode	Behaviour
Off (Ungrouped)	Each image is independent; no plate/well view is shown
Filename	Group by regex match on the filename
Foldername	Group by the immediate parent folder name

Filename regex

When Filename grouping is selected, a regular expression is used to extract the well position (row, column) and image index from each filename.

The regex must capture three named groups in order: row (a letter A–Z), column (decimal number), and index (decimal number).

Example regex: _((.)([0-9]+))_([0-9]+)

For filenames like sample_A1_1.tif, sample_A1_2.tif, sample_B3_1.tif this extracts:

• Row: A / B
• Column: 1 / 3
• Index: 1 / 2 / …

Caution

Grouping settings cannot be changed after an analysis has been started. If you need different grouping, re-run the analysis with the corrected settings.

Well order matrix

The Well order matrix controls how individual images within a well are laid out in the results image view. The default [[1,2,3,4],[5,6,7,8],[9,10,11,12],[13,14,15,16]] places image index 1 in the top-left, index 2 to its right, and so on.

Plate Size

Select the microplate format (6-well, 12-well, 24-well, 96-well, …). Open the Plate settings dialog to define the well labelling order.

Z-Stack Handling {#z-stack}

Setting	Behaviour
SingleStack	Analyse only the selected Z index (default: 0)
AllStacks	Run the pipeline independently for every Z plane
MaxIntensity	Collapse all Z planes with a maximum-intensity projection
MinIntensity	Collapse with a minimum-intensity projection
AvgIntensity	Collapse with an average-intensity projection
SumIntensity	Collapse with a sum-intensity projection
TakeTheMiddle	Use the Z plane nearest to the centre of the stack

When MaxIntensity (or any other projection) is selected, each pipeline must additionally specify which projection mode to use for its input channel.

T-Stack Handling {#t-stack}

Setting	Behaviour
SingleStack	Analyse only the selected time frame (default: 0)
AllStacks	Run the pipeline independently for every time frame

When AllStacks is selected you can also set a Playback speed (frames per second) for the image viewer.

Tile Size

For very large images (whole-slide imaging), EVAnalyzer automatically splits the image into tiles. The tile width and tile height settings (default: 4096 × 4096 px) control the maximum tile size loaded into RAM at once.

See Image Formats — Big Images for details.