Output files

Spotmax output files include segmentation, tabular, and processed image data.

Segmentation and processed image data will be saved in each Position_n/Images folder.

Tabular data will be saved in each Position folder in a sub-folder called SpotMAX_output.

Segmentation data

Segmentation masks are saved from spots and reference channel data. These data are optional and can be saved by activating the parameters Save spots segmentation masks and Save reference channel segmentation masks, respectively. The default size of the spots masks is explained here. If you need spot masks with different sizes, you can specify which features to use with the parameter Features for the size of the saved spots masks.

The naming pattern is the following:

<basename>_run_num<run_number>_<spots_ch_name>_spots_segm_mask_<_spot_size_feature_><appended_text>.npz
<basename>_run_num<run_number>_<ref_ch_name>_ref_ch_segm_mask_<appended_text>.npz

where <basename> is the common part of all the file names in the Position folder, <run_number> is the run number defined at Run number, the <spots_ch_name> is the text provided at the Spots channel end name parameter, <ref_ch_name> is the text provided at the Reference channel end name parameter, <appended_text> is the text provided at the Text to append at the end of the output files parameter, and <_spot_size_feature_> is empty for the default spot size, or the name of the feature used for the spot masks size provided at the parameter Features for the size of the saved spots masks.

Tables

In the SpotMAX_output folder you will find the following set of tables:

<run_number>_0_detected_spots_<appended_text>.<ext>
<run_number>_0_detected_spots_<appended_text>_aggregated.csv
<run_number>_1_valid_spots_<appended_text>.<ext>
<run_number>_1_valid_spots_<appended_text>_aggregated.csv
<run_number>_2_spotfit_<appended_text>.<ext>
<run_number>_2_spotfit_<appended_text>_aggregated.csv
<run_number>_3_ref_channel_features_<appended_text>.csv
<run_number>_4_<source_table>_<input_text>_<appended_text>.<ext>
<run_number>_4_<source_table>_<input_text>_<appended_text>_aggregated.csv
<run_number>_analysis_parameters_<appended_text>.ini

where <run_number> is the number selected as the Run number parameter, <appended_text> is the text inserted at the Text to append at the end of the output files parameter, and <ext> is either .csv or .h5 as selected at the File extension of the output tables parameter.

See also

For the file <run_number>_3_ref_channel_features_<appended_text>.csv see more details in the description of the Save reference channel features parameter.

For the files <run_number>_4_<source_table>_<input_text>_<appended_text> see more details in the Inspect and edit results section.

The file with analysis_parameters in the name is the INI configuration file with all the parameters of that specific analysis run.

The files ending with _aggregated contain features related to the single segmented objects (e.g., the single cells) as described in the section Aggregated features description, while the other files contain the features related to the single spots as described in the section Single-spot features description.

Additionally, 0_detected_spots means that the file contains all the detected spots without any filtering, while 1_valid_spots means that the file contains the spots after filtering based on the features selected at the Features and thresholds for filtering true spots.

Note

The file 0_detected_spots might also contain spots that are outside of the segmented objects. This is by design, because the idea is to save all the detected spots. These spots will appear in the table with the column Cell_ID equal to 0.

Finally, the file with 2_spotfit will be created only if Compute spots size (fit gaussian peak(s)) paramter is True. This file contains additional features determined at the spotFIT step, as described in the section SpotSIZE metrics.

Concatenate multiple experiments results into single file

If you are using the same data structure required by Cell-ACDC you can concatenate multiple Positions and multiple experiments results into a single table.

To do so, run Cell-ACDC and in the small launcher window go to the menu on the top menu bar Utilies --> Concatenate --> Concatenate SpotMAX output tables....

Select as many experiment and Position folders as you need and, optionally, select if you need to copy cell cycle annotations from the Cell-ACDC output file.

The multiple Positions final table will be saved in each experiment folder selected in a folder called SpotMAX_multipos_output. The table will have an additional column called Position_n that indicates from which Position the data on each comes from.

If you select more than one experiment folders, Cell-ACDC will also create a table with the all the results from each Position and each experiment selected. The table will be saved in a folder of your choice (you will be asked to select it) and it will have two additional columns called experiment_folderpath and experiment_foldername to identify where the data come from.

Processed image data

Pre-processed images are saved from spots and reference channel data. These data are optional and can be saved by activating the parameters Save pre-processed spots image and Save pre-processed reference channel image, respectively.

The naming pattern is the following:

<basename>_run_num<run_number>_<spots_ch_name>_preprocessed_<appended_text>.<ext>
<basename>_run_num<run_number>_<ref_ch_name>_preprocessed_<appended_text>.<ext>

where <basename> is the common part of all the file names in the Position folder, <run_number> is the run number defined at Run number, the <spots_ch_name> is the text provided at the Spots channel end name parameter, <ref_ch_name> is the text provided at the Reference channel end name parameter, <appended_text> is the text provided at the Text to append at the end of the output files parameter, and <ext> is the extension of the input channel file.