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--- how_to_upload_slides [2025/08/13 16:38] – rudy
+++ how_to_upload_slides [2026/03/23 11:20] (current) – rudy
@@ Line 1: / Line 1: @@
 ====== How to Upload Slides ======
-There are several options available for users to upload slides from local disks to the My Pathomation cloud. Each has advantages for specific use cases and specific file formats.
-**Important Note:** **Some whole slide image types consist of multiple files & folders which require joint context to be read correctly. \\
+**Important Note:** Some complex whole slide image types consist of multiple files & folders which require joint context to be read correctly. These include .mrxs, .isyntax, .mds, .mdsx, .dzi,.vsi, … The My Pathomation software upload process verifies the integrity of the files and will warn you in case of missing files.\\
-These include .mrxs, .isyntax, .mds, .mdsx, .dzi,.vsi, …\\
+{{ ::v3.1.0_missing_upload_file_warning.png?200 |}}
-If you are uploading these filetypes use the transfer from local to cloud function described under heading #3 for ease of use**\\
+If you are uploading these filetypes use the transfer from local to cloud function described under heading #3 for ease of use\\
+There are several **options available for users to upload slides** from local disks to the My Pathomation cloud. Each has advantages for specific use cases and specific file formats.
 {{ :3.0.2_upload_options_1_2_3.png?600 |}}
@@ Line 14: / Line 15: @@
 {{ :grundium_x_my_pathomation_.mp4 |}}
+When your upload starts a pop-up notification shows under the status icon
+{{ :v3.1.0_status_notification_icon.png?200|}}
+When the process completes a new pop-up appears. Clicking on the icon will show a live status of the process.
 **2. The Blue Upload Button**
@@ Line 24: / Line 30: @@
 **3. The Local / Cloud Browser**
-My Pathomation also works as a viewer for local images with the addition of PMA.start. If you have not already done so, you can download this here https://www.pathomation.com/free-desktop-viewer-pma-start/.
+My Pathomation also works as a viewer for local images. When it comes to complex whole slide image types, looking through the eyes of the local viewer you always see one image, the software groups all subfolders and data files also for uploading, avoiding you to go and copy each relevant file contributing to complex whole slide image types.
+You can see the local folder structure in the 'Local' tab and open all the images stored on your Hard disk or USB drive(s). The 'Local' tab also allows you to select images and upload them to your cloud storage in the 'Cloud' tab.
+PLease note that for this function you need the **PMA.start component**. If you have not already done so, you can download this here https://www.pathomation.com/free-desktop-viewer-pma-start/.
+Uploading one slide can be done by clicking the cloud icon next to the image
+{{ :3.0.2_upload_via_local_view.png?600 |}}
-Once installed, you can see the local folder structure in the 'Local' tab and open all the images stored on your hard drive(s) or USB storage. The 'Local' tab also allows you to select images and upload them to your cloud storage in the 'Cloud' tab.
+Mulitple slides can be selected and uploaded at once if you follow these steps
+{{ :3.0.2_upload_via_local_view_multiple.png?600 |}}
-{{ :How to upload slides_3_select local.png |}}
 **4. The Upload Function in PMA.start**
@@ Line 35: / Line 49: @@
 To explore this function we refer to the PMA.start wiki page  https://docs.pathomation.com/pma.start/doku.php?id=upload
+Advanced user tip
+The single file formats can also be upgraded to multi-file formats. Hamamatsu scanners can create .ndpis files for fluorescent or z-stacked content. The “s” stands for “set”: the .ndpis file merely contains pointers to individual .ndpi files which then each contain the image for the particular layer or channel.
+**Blog Article** https://realdata.pathomation.com/what-wsi-data-are-really-made-of/#:~:text=Several%20vendors%20have%20adopted%20a%20single%20file%20format,include%203DHistech%20%28MRXS%29%2C%20Olympus%20%28VSI%29%2C%20and%20Motic%20%28MDS%29.