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--- how_to_upload_slides [2024/11/20 09:12] – chris
+++ 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.
-**Important Note:** **Some whole slide image types have a complex folder structure (e.g. .mrxs, .isyntax,…) which require the full folder context to be read correctly. If you're working with these filetypes proceed straight to heading #2**
+**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.\\
+{{ ::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\\
+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 |}}
 **1. The Drop Zone**
-This will allow you to drag and drop images from your local folders.(1)\\
+This will allow you to drag and drop images from your local folders.(1). Simply drag your file or files from your local storage hold it over the dropzone and release it for upload. Have a look at this video with an example from Grundium slide scanners.\\
-**2. The Blue Upload Button**
+{{ :grundium_x_my_pathomation_.mp4 |}}
-The blue upload button (2) opens a dropdown menu in which you can select whether you’d like to upload files or whole folders (3)\\
+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**
-{{ :How to upload slides_2_blue upload and drop box.png |}}
+The blue upload button (2) opens a dropdown menu in which you can select whether you’d like to upload files or whole folders (3). This function is very useful if you have a whole folder to upload.\\
-The whole folder upload (3) is necessary for multi-file formats including (but not limited to): .VSI .mrxs .dzi and .isyntax.\\
+{{ :3.0.2_upload_button.png?600 |}}
-A couple of good indications if your filetype is multi-file:
-  * It has a stacked folder - the folder has the same name as the scan, and there are several files in the folder which have the same tissue sample on.
-  * There will be several filetypes in the same folder.
-{{ :upload folder.png |}}
 **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://free.pathomation.com/ .
+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 37: / 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.