# Dataset Title (meaningful, descriptive)

**PI:** Prof. Dr. Jane Doe, [jane.doe@example.com](mailto:jane.doe@example.com), Head of Department X

**Experimenter:** John Doe M. Sc., [john.doe@example.com](mailto:john.doe@example.com)

**Project:** Observing freshly forming pits in the cell membrane of PC12 cells using ultrasonic membrane-sheeting technique, focusing on synaptic specific proteins involved in exocytosis. Images will be taken on a custom build Nikon Widefiled SD-dSTORM Microscope. Protocol follwoing *Example Scientist et al.*, 2025, Example Neuro Journal, DOI: [10.1111/example.1234567](https://example.com/10.1111/example.1234567); and documented (including mounting and dSTORM buffer) in detail at `Reference` (e. g. Link or just internally reachable Server location like `Server:\Group\Protocols\dSTORM_buffer`)

**Software:** NeuroSheet ImageJ Plugin can be found here: [example.com/Neurosheet](https://example.com/neurosheet), setting for SD-dSTORM reconstruction will be provided in `sdmixer.ini` in the same directory this README.md file is located.

---
## File Naming Convention

```
SType_StainX_Illu_PARAM_SampID_STATE_AAA.XXX

SType     Whole (whole PC12 Cells), 
          Sheet (Membrane sheets of PC12 cells by applying ultrasound)
StainX    (ALWAYS: Focal Adhesion Alexa 488)
          Stain1 (Clathrin Heavy Chain (CHC) Alexa 647, Synaptotagmin (Synt) DF 678)
          Stain2 (Synaptobrevin (Synb) Alexa 647, Syntaxin-1 DF 678)
          Stain3 (Dynamin (Dyn) Alexa 647, SNAP-25 DF 678)
          Stain4 (Syntaxi-1 Alexa 647, Dyn DF 678)
          Stain5 (Synb Alexa 647, CHC DF 678)
          Stain6 (Synt Alexa 647, SNAP-25 DF 678)

Illu      (Illumination)
          WFld (Widefiled), 
          HiLo (Highly inclined thin illumination), 
          TIRF (Total Internal Reflection).
PARAM     5 Digit Entry, 00000 if not relevant (e.g. Wide Field) or applicable Parameter (TIRF or HiLo Angel as a 5 digit read out from "TIRF-Position-Angle" in NIS Software).
SampID    Sample ID: Identifier from which batch of cells sample was derived, e. g. WP0704
STATE     rawda (raw data, usally ND2 or TIFF image stack),
          local (localization list, usally csv), 
          recon (SD-dSTORM reconstruction, usally TIFF), 
          2Dhis (2D Histogram of spectral demixing intensities, usally TIFF or PNG)
AAA       Sequencial Number
.XXX      nd2 (Nikon NIS-Elements Software Image Format)
          csv (comma-separated values)          
          tif (OME-TIFF)  
          png (Portable Network Graphics, Image File)
```
### Examples files names:

An images of a whole PC12 cell with the fifth staining: Focal Adhesion Alexa 488, Synaptobrevin (Synb) Alexa 647, Clathrin Heavy Chain (CHC) DF 678; Recorded under TIRF illumination; TIRF-Angle-Value in NIS: 4500; Cell Culture ID: NC0877; the raw data image stack, sequencial number 003 and direclty from the microscope in the ND2-File-Format. 

`Whole_Stain5_TIRF_04500_NC0877_rawda_003.nd2`

Different Examples:

`Sheet_Stain1_HiLo_01250_NC0865_2Dhis_006.png`

`Whole_Stain3_Wfld_00000_NC0877_rawda_004.nd2`

---
## Description of Folder Structure

The files are organized in the follwoing folder-Structure

```
PC12-superres-Project02/
└── {YYYY--MM-DD}/
```

Later the data from several dates is pooled in a single folder, but separated by SType (Whole or Sheet). The First part of the filename will determine in which folder the files will go, see above under file names for conventions. Raw and processed data stay together in the same folder.

```
PC12-superres-Project02/
├── Whole/
│   ├── Whole_StainX_Illu_PARAM_SampID_STATE_001.XXX
│   ├── SType_StainX_Illu_PARAM_SampID_STATE_002.XXX
│   ├── ...
│   ├── README.md
│   └── ...
└── Sheet/
    ├── Sheet_StainX_Illu_PARAM_SampID_STATE_AAA.XXX
    └── ...
```
Copy of the raw data files are saved in OMERO at [omero.charite.de/webclient/?show=project-example](https://omero.charite.de/webclient/?show=project-example)