Use .loc instead .at

            fn = self.fileList.item(index, 5).text()

            # Identify row by filename (better than index)

            item = self.df.loc[self.df['filename'] == fn]

            item_index = self.df['filename'] == fn

            self.df.at[item.index, 'processed'] = True

            self.df.loc[item_index, 'processed'] = True

            self.fileList.setCellWidget(index, 2,

                                   self.getIconCell(True))

            for radio in self.rbTypes:

                if(self.rb[radio].isChecked()):

                    self.df.at[item.index, 'morphology'] = radio

                    self.df.loc[item_index, 'morphology'] = radio

                    break

                else:

                    self.df.at[item.index, 'morphology'] = utils.getMorphology()[-1]

                    self.df.loc[item_index, 'morphology'] = utils.getMorphology()[-1]

            for column in self.cbColumns:

                self.df.at[item.index, column] = self.cb[column].isChecked()

                self.df.loc[item_index, column] = self.cb[column].isChecked()

            self.df.at[item.index, 'comment'] = self.commentBox.toPlainText().replace('\n', '')

            self.df.loc[item_index, 'comment'] = self.commentBox.toPlainText().replace('\n', '')

            self.fileList.selectRow(index+1)